The Justice Department is investigating allegations that several Environmental Protection Agency officials ordered the destruction of potentially embarrassing documents in a file that had been requested by Congress, according to officials familiar with the case.

According to agency correspondence, John P. Horton, who was fired in February as the EPA's assistant administrator for administration, decided to dispose of summaries of an FBI background investigation of an EPA nominee whose name had been withdrawn. Several officials said that Horton last summer ordered the agency's security office to destroy the documents.

Former general counsel Robert M. Perry authorized and defended Horton's move to dispose of the FBI summaries before they could be turned over to Rep. James H. Scheuer (D-N.Y.), according to the EPA correspondence.

Knowledgeable sources said that EPA acting Inspector General Charles L. Dempsey has asked Justice to determine whether the destruction of the federal documents constitutes an obstruction of justice.

Dempsey declined to comment. But sources said he also has asked Justice officials to examine the role played by EPA deputy general counsel Gerald H. Yamada, the agency's ethics officer; Yamada's assistant, Donald Nantkes, and the former inspector general, Matthew N. Novick. Justice is investigating whether they knew of the discussions.

Justice officials must decide whether to refer the latest allegations to a federal grand jury that has been investigating possible perjury and conflicts of interest by several EPA officials who have left the agency in recent months.

Yamada said yesterday that he had recommended against destroying the files, but that the EPA's security chief later told him that "he was ordered to do it." Yamada said security officials told him that Horton gave the order.

Horton's attorney, Philip Kellogg, said Horton was in Europe and that Kellogg has not been informed of the allegations. Efforts to reach Perry at his Washington apartment were unsuccessful.

Nantkes said he never participated in such discussions. "I deny that," he said.

The incident began last June when Scheuer, chairman of a House Science and Technology subcommittee, asked for the EPA's personnel file on Peter Krenkel, whom then-EPA Administrator Anne M. Burford had planned to nominate as assistant administrator for research.

After an FBI background check on Krenkel, Burford had decided not to submit his name for the post, but instead made him a senior consultant in the research office, where he continues to work part time.

The FBI report said that Krenkel had been fired from his job as environmental planning director at the Tennessee Valley Authority and that he had been banned from flying on Delta Airlines because of previous behavior on flights, according to an EPA memo describing Krenkel's response to the FBI report.

The May 5, 1982, memo by EPA acting security chief Donald E. Kraft said that "Krenkel was advised that the FBI investigation contained information that he was barred from flying Delta Airlines as a result of a few incidents where he had been inebriated and accosted flight personnel . . . . Krenkel flatly denied that any such incidents ever occurred and plans on contacting Delta to straighten out the matter." Krenkel also said the firing was "politically motivated," the memo said.

Krenkel, who is engineering school dean at the University of Reno, said yesterday he did not know about the FBI report and did not want to discuss the charges. "All I did was work my tail off at the EPA," he said.

In a letter to Scheuer last June, Horton said he would not turn over part of Krenkel's file because Krenkel no longer was a possible nominee. Horton noted that the file "contains a summary of an FBI background investigation on Dr. Krenkel," but he said he had determined that this was not within the scope of Scheuer's request.

Two months later, Perry wrote to Scheuer saying Horton had been unaware that the agency kept the FBI summaries on people who no longer were candidates for high-level jobs.

In that letter, Perry said Horton had decided that "EPA no longer retains background summaries in cases where the subject is not under consideration for a presidential appointment, including the background summary for Dr. Peter Krenkel."

Yamada said that he, Perry and Nantkes continued to discuss what to do with the FBI summaries. "Bob Perry knew about this every step of the way," he said. ". . . Any advice we gave was run by Perry."

Although the EPA later gave Scheuer other documents, Yamada said that when he heard that Horton ordered the FBI summaries destroyed, "I was very upset about that . . . . I think it was poor judgment to get rid of it."

Justice is still probing allegations, made shortly before Horton's firing in February, that he was performing work for several private businesses in his EPA office. Horton has said he did the work on his own time.

Novick, who also was dismissed in February, declined to comment.

Also this week, Dempsey charged in an unrelated report that the inspector general's office has been unable to investigate fully possible wrongdoing at EPA because of interference from top agency officials.

Dempsey said investigators "cannot even begin to scratch the surface" of alleged fraud at EPA.

Dempsey said that Burford's aides opened confidential letters from members of Congress to his office and would not allow replies to be sent without their approval. He said Burford did not allow investigators to be hired without her approval.