City Administrator Elijah B. Rogers yesterday reassigned a city permit examiner who allegedly lowered permit fees after accepting personal payments from three applicants, and launched an internal investigation into possible wrongdoing by the examiner, Warner B. Jenkins.

Rogers said that Jenkins had been relieved of his duties, placed under the direct supervision of the agency head, Lacy C. Streeter, and instructed to write a report of his actions for city investigators. Also reassigned, Rogers said, was Jenkins' supervisor, W. Monroe Stewart, acting deputy chief of the construction section of the Department of Housing and Community Development, pending the outcome of the city's investigation.

Meanwhile, a team of four FBI agents continued to sift through permit records in D.C. government offices at 614 H. St. NW as part of an investigation that began earlier this week after one person who said he made a payment to Jenkins informed the U.S. attorney's office of his action.

Rogers' actions came in response to a story in Thursday's editions of The Washington Post report that Jenkins, 47, three times lowered permit fees after receiving personal payments from applicants, according to canceled checks, documents and those who said they paid him.

Jenkins denied any wrongdoing and said that any money he might have accepted would have been for interior design work unrelated to the applications. Jenkins said he does such work in addition to his $24,527-a-year city job.Two persons who said they made payments to Jenkins told reporters that no such design work was done or discussed. A third person who said he made a payment to Jenkins could not be reached for comment.

Numerous architects, however, homeowners and contractors told The Post that the city's system for issuing permits was lax, and that applicants routinely undervalue renovation project costs and thus reduce the fees they pay the city. The project costs are the basis for the fees to the city, which assesses $38 for each estimated $1,000 of renovation work.

A review of city records and numerous interviews found frequent instances where estimated costs were lowered, resulting in lower fees paid to the city. In all but those three instances, there were no indications that any personal payments were made.

City Housing Director Robert L. Moore said yesterday that he was unaware of any pattern of undervaluing projects in obtaining renovation permits. "We're going to be doing a review of the entire fee-setting process on permits," Moore said. "We want to see exactly what is being done."

Moore said that city officials had no information that Jenkins or any other city officials had done anything wrong. "All we have is what we read in the newspaper," Moore said. He said Stewart was also reassigned only because he was Jenkins' direct supervisor.

Moore said he has ordered Streeter, administrator of the Building and Zoning Regulation Administration, to approve and initial any revisions to project costs. Previously, those revisions were approved only by Jenkins, Stewart or one of the other two structural engineers who worked under Stewart's supervision.

In a further attempt to tighten permit procedures, Carol Thompson, acting director of the D.C. Department of Licenses, Investigations and Inspections, said she ordered a review of any related actions in her department, which formally issues the permits.

Thompson also said that more specific guidelines for applicants would soon be developed that would define what is to be included in project cost estimates. No such guidelines now exist, and there are different interpretations of what costs should be included in the estimate. a

The three incidents in which Jenkins allegedly received improper payments took place between November 1980 and March 1981.

The first involved Brian Fitzpatrick, who obtained a permit for renovation of his row house on Capitol Hill on Nov. 13, 1980. Jenkins lowered the estimated value of the renovations from $30,000 to $3,000, reducing the fee by more than $1,000, according to city records.

Fitzpatrick said he wrote one check to the D.C. Treasurer for the fees and another for $250, which he made payable to himself, endorsed and then gave to Jenkins. Fitzpatrick said the canceled check was endorsed with 'Jenkins' name and deposited, but he declined to show the check to reporters.

In the second incident, Helmut Hawkins, a federal government employe, told reporters that last Dec. 9, Jenkins lowered the estimated value of renovations proposed for his town house in Mount Pleasant from about $14,000 to $2,000. That lowered the permit fee from about $500 to $76.

Hawkins said he paid the fee and also gave Jenkins another check for $75, which was later endorsed with Jenkins' name and deposited. Hawkins gave both checks to two reporters of The Washington Post.

The most recent incident involved Tony Ruggerio, a construction employe for McDonald's Corp. Ruggerio told reporters that in March, Jenkins lowered the value of proposed renovations on a restuarant downtown from $45,000 to $25,000. Ruggerio said Jenkins instructed him to make the check for the permit fee, $950, payable to Jenkins instead of the city treasurer.

Ruggerio later became suspicious, he said, stopped payment on that check drawn on his personal account, and wrote another one to the D.C. Treasurer for the same amount.

City Council member Charlene Drew Javis (D-Ward 4), chairman of the council's committee on housing and economic development, said yesterday that she plans to investigate whether there is a pattern of undervaluation on construction work and whether there is any corruption in the permit process.

"There are potentially a dozen places along ther permit process where it could happen," she said.

Jarvis said one way to tighten permit procedures would be for the city to have someone whose sole job would be to review the value amounts set on all construction and renovation permits. At present, the structural engineers have dual responsbilities to review the structural integrity of proposed renovation projects and to set the fees after determining costs.

Jarvis said her committee would seek testimony from building and zoning officials to explain how corruption like that alleged could take place.

"We will be looking at reducing the number of steps in the permit process, and thus reducing the opportunities for people who are dishonest to get this kind of payoff," Jarvis said.