Attorney General Griffin B. Bell said yesterday that the federal corruption investigation of Rep. Daniel J. Flood (D-Pa.) includes "possible abuses" of employes in three Justice Department agencies.

Bell made the disclosure in a letter that accused Sen. Malcolm Wallop (R-Wyo.) of having jeopardized investigations by disclosing that the Justice Department itself was involved in the Flood inquiry.

"Walop read to reporters after a hearing Thursday from a department letter that referred to a grand jury investigation "into fraul and corruption involving Flood and several federal agencies, including the Department of Justice."

Bell's letter to James O. Eastland (D-Miss.), chairman of the Senate Judiciary Committee, complained that Wallop's action was a "gross breach" of a committee agreement with the department over access to records relating to the dismissal of Philadelphia U.S. Attorney David M. Marston.

Wallp has been using the hearings on Benjamin R. Civiletti's nomination to be deputy attorney general to examine the Marston ouster.

He said yesterday, through an aide, that his citing of the controversial passage was inadvertent. But Wallop does not consider his action a breach of the agreement, the aide added.

And in a letter being drafted in response to Bell's, the senator charged that Bell himself "elaborates and provides us with details" on the department's involvement.

In a footnote in his letter, Bell said, "The reference to the Department of Justice relates to possible abuses by others of employe personnel of LEAA, Bureau of Prisons and FBI."

Department officials yesterday declined to elaborate on the footnote except to say that the allegations were still being checked out and department employes were not targets.

Stephen B. Elko, a former Flood aide who has turned government witness, has charged that the 74-year-old chairman of a key House Appropriations subcommittee has traded his influence for more than $100,000 in cash over the years.

Flood and Rep. Joshua Eilberg, another Pennsylvania Democrat, have both been under investigation in connection with federal funding for a Philadelphia hospital. Marston's office as well as an organized crime strike force in Washington, have been conducting the investigation.

Civiletti said yesterday that the footnote was placed in Bell's letter because Wallop's unexplained disclosure made it appear that main Justice Department prosecutors might be improperly involved in the investigation.

In a related development yesterday, Wallop said he was writing President Carter asking for sworn affidavits from five White House aides about their knowledge of a call from Eilberg last November that urged Marston's dismissal.

Included are Hamilton Jordan, the president's closest political adviser, and Frank Moore, the chief congressional lobbyist at the White House.

Carter, meanwhile, told a group of out-of-town newspaper editors that the Marston case had turned out to be "a very serious problem for us and I regret that it happened." He said if he had known more about it, he would have "handled it more expeditously and more openly and frankly."

He told a press conference soon after the dismissal that he wouldn't have done anything differently.