The stench is gone, and so are the flies and cockroaches. The bodies, once piled on top of one another, now lie neatly on fiberglass and metal trays. The dead come and go efficiently. Change is in the air at the D.C. morgue, 17 months after Jonathan L. Arden arrived as chief medical examiner--a job no one in his profession wanted.

The lanky, bearded, 45-year-old forensic pathologist from New York has reformed with a vengeance. He has reduced the backlog of unclaimed bodies and set up stricter autopsy criteria for suspicious deaths, especially of children. He is trying to fire two of the office's seven forensic pathologists. He has dismissed or placed on leave the morgue's two office administrators and the senior autopsy technician.

But his efforts at overhauling one of the District's most troubled agencies also have fostered a climate of distrust and apprehension. The remaining staff is on the verge of open revolt--most of them have asked Mayor Anthony A. Williams (D) to remove their boss. Many on the staff say the improvements in the office have been attained only by overworking employees in a morgue that even the medical examiner himself admits is still filthy and unhealthful.

In a series of interviews, Arden brushed off the criticism and instead attacked what he called a "frustrating and mystifying" culture of dysfunction. "I've come in from the outside. I have no ties to the prior history and culture of the D.C. government and regime," Arden said. "I am a no-nonsense guy, and I am sick and tired of the nonsense--this is the nicest thing I can think of for other, stronger words that describe what goes on here every day."

The tough-talking doctor, who headed Brooklyn's morgue before coming to the District, said he "shook some things up" by imposing a standard of accountability to which many in the office had not been held before. The agency was filled with "inappropriate and unacceptable" work practices, Arden said. His public assessment of his staff is unusually critical and blunt, unique among the coterie of outside administrators who have been brought in over the last few years to salvage critical city agencies.

"We have some very seriously disgruntled employees," Arden said. "Why are the people unhappy? Because they're being held to levels of accountability they've never been held to before. I've upset the apple cart. Well, get used to it."

The medical examiner's office performs a vital function, not only for the criminal justice system but also for the public's health. It is a clearinghouse for information on drug use, suicides, infectious diseases and other important health indicators. It now conducts more than 1,200 autopsies a year, about 80 percent of all deaths reported to it and about 100 more than in previous years, Arden said. The staff has grown to 44 from fewer than 30 last year, and the annual budget has jumped to $4.2 million from $3.3 million.

The morgue, which has an official capacity of 58 bodies, contained 60 on a recent morning. Arden hopes to reduce the number further by having regular pickups of unclaimed corpses. A private firm now performs cremations, so the crematorium sits unused. Scattered in front of it are dozens of wooden boxes once used to store ashes.

The doctor has started a case-tracking system to record all deaths reported to the office. He has offered month-long internships to medical students from George Washington University. He has increased the proportion of bodies that are autopsied, ordering dissections on all chronic alcoholics and psychiatric in-patients, two groups likely to have unnatural causes of death.

Arden was hired in April 1998 by the District's then-chief management officer, Camille C. Barnett, who offered him $165,000 a year to lead an agency that had been leaderless for six years in the 1980s and had been threatened with a Justice Department takeover. Arden said he was prepared for the challenges, but he also acknowledged that the obstacles were greater than he expected. Data keeping was irregular. The office didn't record cremation approvals or note deaths that were reported but not investigated further. Lines of responsibility were unclear, and devoted employees worked alongside lazy ones, Arden said.

"We had people here who were actively insubordinate and intransigent and subverting the process," he said. "We had people here who were marginally competent and some who were incompetent."

The chief medical examiner's office historically has been hampered by its lack of political representation in the city, said Joshua S. Wyner, executive director of the D.C. Appleseed Center, which released a report last year that recommended that the office be governed by an oversight commission. James L. Luke, who helped draft that report, said the office suffered from a decade of neglect. "There was a general lack of interest in the office over the span of many years," said Luke, who was the District's coroner and then its first chief medical examiner from 1971 to 1983.

When Barnett left in January, Arden, by his own admission, spent more time at the mayor's Cabinet table than at the autopsy table, working to build political support. He has made inroads. The mayor has elevated the chief medical examiner to Cabinet-level status, and Arden hopes eventually to take the office from under the Department of Health and make it an independent city agency. That process, which would require D.C. Council approval, could take several years.

But inside the squat brick building, change has not come easily.

Complaints followed the firings and the hirings of senior staff members from the outside, including Jacqueline A. Lee, the deputy chief medical examiner, and George Randall Moshos, the director of investigations, a new position. Arden declined to discuss individual personnel cases but said all the terminations were justified.

Staff members at the morgue say the increased workload has worsened already unsafe and unsanitary conditions in the autopsy room and refrigeration unit. They say that Arden's criticism of the office has demoralized the staff.

"The morale has dropped to the lowest level in the past 15 years," according to a memo signed by 24 of the office's 44 employees and sent last month to Williams and other city officials. "We are constantly insulted and accused of being incompetent, threatened to be removed from our positions, berated, harassed, belittled and disrespected."'

As for Arden, the memo said: "We are often overworked and the Chief never, ever steps forward to contribute or give a word of thanks or compliment. It appears he only knows negative criticism."

At a July 15 staff meeting that particularly upset employees, Arden told the staff, "If you're not happy or don't like what's going on, you can look in the classifieds." Arden later said he meant to emphasize the need for "stricter and more stringent professional standards."

"The staff is being treated unfairly," said Abdul-Raheem Abdullah, who was fired July 30 as the agency's director of operations and has become an unofficial spokesman for unhappy employees. Abdullah said many are irked more by Arden's imperious style than by the increase in work.

"You're scared to say anything," said an employee who transcribes the doctors' notes. "You don't know if you're the next one who's going to be fired." Like others, the worker agreed to speak only if not identified.

An occupational safety and health inspector from the D.C. Department of Employment Services visited the morgue last month after receiving anonymous complaints about safety conditions. Arden was not alarmed. "It's no secret that we're not in compliance" with federal workplace safety standards, he said.

The infrastructure problems are significant. The smaller of two refrigeration units used to store bodies broke down last year. Decomposed corpses from the smaller unit have been placed alongside the "fresh" bodies in the main unit, creating a pungent odor. Arden said separating the bodies would have been "convenient" but not cost-effective.

Ventilation in the morgue is poor, leaving stale air sitting in work areas. Bodily fluids continue to collect in puddles in the autopsy room because of clogged pipes. "We don't have ventilation. We're working massively understaffed, massively underpaid," said an autopsy technician.

A planned $2.5 million renovation would revamp 75 percent of the 23-year-old building, installing a new ventilation system, a new X-ray facility, and specimen and evidence storage areas. The renovation is behind schedule, but Arden said he hopes to award a contract this month and complete the work in the next 12 months.

Of the seven medical examiners, just three, including Arden and Lee, are certified by the American Board of Pathology. Although not legally required in the District, certification is commonplace in major cities, according to John E. Pless, a professor of pathology at Indiana University and past president of the National Association of Medical Examiners. The office's own certification with the medical examiners association has lapsed, but Arden hopes to renew it.

Arden's decision to hire three physician assistants to work as "medico-legal" investigators on the one-quarter of autopsy cases that are homicides also has caused grumbling among police detectives accustomed to working the cases alone. Arden said the move, which is supported by senior police officials, added a critical component to solving cases.

The mayor's office hasn't responded to the employees' memo. Williams is scheduled to meet with the staff Sept. 28 at a brown-bag lunch at which Arden will not be present, said Peggy Armstrong, a mayoral spokeswoman. But the interim city administrator, Norman Dong, said Arden has the mayor's support.

"He was brought in to reform a dysfunctional operation, and he's doing exactly that," Dong said. "And any time you make major reforms, you're going to ruffle some feathers. We cannot be distracted by those people who are more interested in maintaining the status quo than in promoting change."

Those encouraging words are echoed by outside analysts. Appleseed's Wyner said morale at the office might grow to be a significant problem, but he urged employees and residents to give Arden "the benefit of the doubt."

"I would be wary of disgruntled employees at this stage," Wyner said. "The improvements in the office have got to be the bottom line for residents of the District of Columbia."