Last month, in a secret military trial in a windowless room at Arlington Hall Station, seven Army colonels found Col. James E. Longhofer guilty of dereliction of duty, disobeying a lawful order and conduct unbecoming an officer. His sentence: two years in prison, a $24,000 fine and an official reprimand.

It was one of a series of closed military trials that has begun at the Army's highly-classified Intelligence and Security Command -- trialsthat raise questions about Army fairness and accountability as well as its ability to run the sort of covert, inventive and fast moving operations that Longhofer, a former head of the service's Special Operations Division, once directed.

The trials issue from a secret, two-year investigation into alleged financial wrongdoing in covert Army operations. One enlisted man has been acquitted, so far, and two officers convicted, one of them Longhofer, a 30-year veteran and father of five, decorated for bravery in combat seven times.

Senior Army officials have declined to discuss details of the investigation, which as one general put it, was brought on by "out of control" officers who got involved in this "James Bond stuff."

But some critics -- including one top Pentagon official -- charge that conventional rules are being applied in hindsight to unconventional operations.

As one retired general, who is not under investigation, put it, Longhofer's offenses seemed "errors in judgment -- if that. I would say they were just an alternate way of doing something."

The Special Operations Division was set up after the ill-fated attempt to rescue the Iranian hostages in 1980. The aim was to be able to act quickly, creatively and secretly, and that meant being able to end-run the cumbersome Pentagon bureaucracy. Funding for the unit came from Army operational money with the approval of Congress and top civilian and military leaders in the Pentagon. The money was sometimes laundered so there would be no paper trail back to the military. It was a new ball-game for the Army. Financial controls were lax, but the emphasis was on getting the job done.

The unit attracted soldiers with inventive minds and can-do attitudes who didn't mind being called "the crazies in the basement" because of their subterranean quarters in the Pentagon. They called their office "The Zoo."

In the fall of 1983, when the senior Army officers who had set up and supported the Special Operations Division had been replaced by a new Army leadership, trouble erupted. Allegations of financial wrongdoing were made against Lt. Col. Dale E. Duncan, who was running a covert Army mission codenamed "Yellowfruit" under the guise of an Annandale security consulting firm called Business Security International.

The charges, by one of Duncan's subordinates, set off the Army's investigation which gradually expanded into an effort to account for all funds used by the division and other secret units working with it. The Army also called in the Justice Department, which last February charged Duncan in federal court with seven counts of theft and filing false claims in accounting for "Yellowfruit" advances.

Critics complain that members of the Army's investigative team, code-named "Task Force Catalyst Maker," lost documents, compromised the security of operations and failed to record evidence properly.They say investigators, armed with conventional Army rules and regulations about how money is to be spent, failed to take into account that the division was not working under those guidelines.

When secrecy prevails, rumors abound. This case is no exception, with talk that alleged wrongdoing by senior officers is being ignored or punished with a slap on the wrist.

Indeed, the first person court-martialed was Master Sgt. Ramon Barron. Suspended in December 1983, he was charged with fraud involving advances he got for covert missions. Only a few hours of his week-long trial last December were open to the press. He was acquitted.

Three months later a federal jury in Alexandria found Duncan guilty on three counts relating to a $796 plane ticket he used to account for advanced government funds. The government presented evidence that he had gotten the ticket free under an airlines frequent-flyer program. Duncan testified he had forgotten it was free when he submitted it to government auditors. His case is on appeal.

Longhofer's court-martial, nearly 2 1/2 years after he was suspended from his normal duties, came next. Many of his charges, none of which alleged financial misconduct, related to his handling of an initial investigation into the 1983 allegations against Duncan. At that time Longhofer was the division's liaison with the Central Intelligence Agency.

A third court-martial, of Lt. Col. Frederick Byard, is set to begin tomorrow. Duncan and another officer, Lt. Col. Bruce Mauldin, are facing charges by the Army.

Few question the need for a special operations capability, especially given the rise of terrorism as a strategic issue. But there is lively debate in the press, in Congress and in the Pentagon over just how that capability is to be fashioned. But as for the Army, its lengthy and costly investigation and its prosecution of these men is apt to send a message that it is not interested in the kind of flexibility, imagination and daring required for such a capability.

The Army certainly has a right to keep its classified missions secret and a duty to see that public funds are accounted for. But secret trials raise unanswerable questions of whether the military hierarchy is serving itself or the national interest. It also threatens the morale of every soldier who goes out on a career limb by getting involved in covert operations in which money gets accounted for by different rules.

If mutual trust cannot exist between the regular Army and its special-operations units, such a covert capability will be impossible.