The FBI began an investigation yesterday into the use of two shredders at the Environmental Protection Agency earlier this year after the Reagan administration refused to let Congress see numerous documents subpoenaed by a House subcommittee.

Several EPA officials testified under oath before the House Public Works Committee yesterday that they believe neither originals nor duplicates of the documents subpoenaed by Congress were shredded.

As they were testifying, a congressional investigator charged that an EPA official attempted to remove a cart full of 15 boxes of documents from the agency Monday before he was stopped by the agency's inspector general.

An aide to Rep. Mike Synar (D-Okla.), who heads one of six congressional panels investigating the EPA, said the files included both personal and official documents, some of which could be relevant to the ongoing investigation by Congress.

Clay Jones, a spokesman for the EPA, said the employe was routinely disposing of surplus files and had applied for a permit to remove the material. He said there appeared to be no sensitive material involved, but added that the files are still being reviewed.

EPA chief of staff John E. Daniel, the top aide to agency Administrator Anne M. Gorsuch, testified yesterday that sensitive documents being sought by Congress have not been shredded. He said copies have been made and stored in locked files. But Daniel added that the EPA, in addition to Congress, had asked the FBI to conduct an investigation.

"We have written a letter to Deputy Attorney General Edward Schmults asking for a full, complete, independent investigation," he said. "If the FBI performs a complete investigation, I think the questions of the committee and the EPA will be answered."

"This is an important concern not only to the committee, but to the EPA . . . . We want to ensure the integrity of the documents . . . our employes . . . and our program," Daniel said, adding that the FBI began to conduct interviews with agency employes yesterday.

The confrontation over the documents, which led to a historic vote by the House last December to cite Gorsuch for contempt of Congress, focuses on the EPA's handling of the $1.6 billion Superfund program to clean up some of the nation's most dangerous hazardous waste dumps.

Rita M. Lavelle, who had headed the office of Solid Waste and Emergency Response, which has responsibility for the Superfund, was fired by President Reagan on Feb. 7.

According to testimony at yesterday's hearing, the two shredders were brought into this office on Jan. 6 and removed by security personnel on Feb. 10.

Committee Chairman James J. Howard (D-N.J.) yesterday questioned whether the Justice Department will allow the FBI to conduct a full investigation of the use of the shredders.

"The attorney general's response to me yesterday says the FBI will conduct a preliminary inquiry of the matter and then provide a report to the Department of Justice to enable them to determine if any further action is warranted," Howard said. "I do not find this reply satisfactory. It is clear to me that in view of the gravity of the charges raised, a full and immediate FBI investigation is called for."

Daniel said that the 50 employes with access to the sensitive documents have been interviewed and all denied shredding any of the subpoenaed documents.

He said no one is sure exactly what was shredded. Congressional investigators have been told by confidential sources within the agency that the shredders were run day and night, including weekends.

Daniel and EPA attorney Gene Lucero said the agency had mistakenly ordered two extra shredders and needed a place to put them. Lucero said he has been told that "less than half of my staff even used the shredder. Some used it just to see how it worked."

He said that one of the shredders was placed next to the office copying machine and was used often for destroying imperfect copies. But Rep. Elliott H. Levitas (D-Ga.), chairman of the House Public Works subcommittee that prompted the contempt citation against Gorsuch, said the copying machine had been "out of order for some time."

Levitas said, "At the very best, it's got to be one of the stupider actions I've ever heard of--moving a shredder in . . . after a subpoena and a contempt of Congress vote."

Lucero said, "I agree with you . . . . It was a stupid decision . . . but it was not procured for the purpose of destroying any of the documents."

Lucero and other EPA officials also indicated at the hearing that they may be withholding from Congress many more documents than previously indicated. In earlier testimony, EPA officials said they were holding back only 64 documents out of the more than 780,000 pages of information they claimed congressional investigators wanted to see.

But Lucero said yesterday that he has sent EPA general counsel Robert M. Perry nine file-drawer-sized boxes of documents he considers to be "enforcement sensitive" that should not be given to Congress. He added that officials in the 10 regional EPA offices around the country are putting together their records and could have similar quantities of documents that might be declared off limits for congressional investigators.

After Perry goes over the documents, they must also be reviewed by both the Justice Department and the White House before a decision can be made not to turn them over to Congress. But because of the volume, Perry said yesterday, there is already a large backlog.

Perry acknowledged that President Reagan has probably seen no more than a directory of some of the withheld documents. He said the actual review is being conducted by the office of White House counsel Fred F. Fielding.

All the officials testifying yesterday said they have no idea how many documents have been classified so far as "enforcement sensitive," meaning the administration claims their disclosure could harm pending hazardous waste dump cleanup cases, or how many will ultimately be withheld.

Rep. Robert W. Edgar (D-Pa.) demanded to know how the EPA can be sure none of those documents has been destroyed when it doesn't know how many documents are involved. The EPA officials remained silent.