President Reagan appointed several new deputies to Environmental Protection Agency Administrator Anne M. Burford yesterday as the White House sought to quell controversy over the agency's performance.

The president appeared irked when questioned by a reporter about whether a scandal is brewing at the agency. "The only one brewing is in the media that's talking about it," Reagan said, repeating his support for Burford.

Attempting to blunt charges of mismanagement and conflict of interest in the EPA's $1.6 billion toxic waste cleanup program, Reagan named three new assistant administrators and a new inspector general on a temporary basis, and said he would nominate another assistant administrator permanently.

In order to move swiftly, the White House filled all but one of the vacancies with high-level officials from other agencies. These officials will not need new FBI background checks and can report to work immediately. White House spokesman Larry Speakes said Reagan wants to "conduct a wider search" for permanent nominees, although the temporary appointees will also be considered.

It was learned yesterday that FBI agents have begun interviewing EPA employes as part of the Justice Department investigation ordered last week by the president. Neither the White House nor the FBI would comment on the progress of the investigation.

White House officials discussed late Wednesday the possibility of setting up a special commission to investigate the EPA, but they are now "leaning away from that" because of the complications it could create, one official said.

Responding for the first time to attacks from congressional Democrats who are investigating the EPA, the White House singled out Rep. James H. Scheuer (D-N.Y.), who had criticized Reagan for the ouster Wednesday of EPA Inspector General Matthew N. Novick.

A White House official, insisting that he not be identified by name, told reporters at the daily news briefing that Scheuer had actually written to the president last Sept. 16 to call for Novick's ouster. The congressman maintained that Novick's conduct was of "such a gross and flagrant nature" that he should be ousted immediately, according to a copy of the letter.

"So the congressman was either wrong once or was wrong the second time," the White House official said. "It's puzzling to us."

Scheuer's spokesman yesterday complained that the White House had "somehow miraculously found a five-month-old letter" on Novick which, he said, was a "transparent attempt to muddy the waters." The spokesman added that Novick was ousted just when he was "courageously doing his job."

In a statement devoid of comment on the current EPA controversy, Reagan named the new deputies to Burford yesterday, and Speakes insisted that the EPA administrator had been consulted on the appointments. Burford, however, was traveling while the White House held meetings on the appointments on Wednesday. Burford said in San Francisco yesterday, "The president and I are determined to reinvest the public's trust in a program that is critical to the American people."

The appointments announced yesterday are:

* Lee M. Thomas, 38, will replace Rita M. Lavelle as assistant administrator for solid waste and emergency response. Reagan fired Lavelle Feb. 7, publicly raising questions about agency management. Thomas, a high-level official at the Federal Emergency Management Agency, gained recognition by leading a federal task force to handle dioxin contamination at Times Beach, Mo.

* Charles Dempsey, 54, will replace Novick as inspector general. Novick resigned Wednesday under White House pressure, but is expected to get another job as an inspector general, Speakes said. Dempsey is a 26-year veteran investigator who rose through the ranks at the Department of Housing and Urban Development to become inspector general in 1979. His office has been responsible for the indictments of more than 100 HUD employes over the last decade.

* Alfred M. Zuck, 48, will replace John P. Horton as acting assistant administrator for administration. Horton was ousted with Novick on Wednesday. Zuck is a career civil servant who has been at the Labor Department since 1958, and has been assistant secretary for administration and management since 1977.

* Lee Verstandig, 45, will take the new and elevated position of acting assistant administrator for legislation. Lee Modesitt, who previously oversaw legislative affairs at EPA, will become an assistant to Burford. Speakes said the new position will deal with the current six congressional investigations of the EPA. Verstandig is presently assistant secretary of transportation for governmental affairs and is a former associate dean at Brown University.

* Courtney Riordan, 45, currently acting assistant administrator for research and development, will be nominated for the permanent position. Riordan has held a variety of jobs at the agency since 1971.

FBI sources said yesterday that interviews were under way as part of their investigation. They said they had told EPA employes that cooperation is strictly voluntary and that the employes have the right to request confidentiality. But some employes expressed concern that they would be forced to meet with the FBI and that their EPA superiors would have access to transcripts of their interviews.

Asked about these concerns, one Justice Department official said he could understand the employes' feelings. "Any time the FBI swoops down on a government agency, it's very intimidating."