The Justice Department yesterday attempted to lay to rest the last remains of its painful investigation of illegal FBI break-ins stemming from the J. Edgar Hoover era.

In a long-delayed report on an inquiry ordered two years ago, FBI Director William H. Webster said he has censured three agents for their role in withholding information about the extent of the break-ins from congressional investigators and lawyers in a New York civil suit.

Though no names were mentioned in the public report, one of those censured is James Ingram, who was promoted last fall to become special agent in charge of the FBI field office in Chicago.

The break-ins investigation led to the filing of criminal charges against three former top FBI officials in April 1978 for approving the so-called "black-bag jobs." The trail of W. Mark Felt, the bureau's former number two man, and Edward S. Miller, its former chief of intelligence, was to begin Monday after several delays resulting from problems about defense access to national security information. A new trial date is expected to be announced today.

The case against former director L. Patrick Gray III was separated from the Miller-Felt case.

When then-attorney General Griffin B. Bell announced the charges, he told Webster to conduct administrative inquiries to discipline the supervisors and agents who conducted the break-ins and to find out why the congressional investigators were lied to.

In December 1978, Webster announced he was disciplining several top agents who were supervisors, but not the street agents. Though the so-called "cover-up" investigation was completed more than a year ago, Webster did not send it to Attorney General Benjamin B. Civiletti until this February. Asked last October -- when Ingram was promoted -- about the delay, the director said the report had not been a top priority item.

The justice Department prosecutors who conducted the original break-ins investigations -- and then resigned from the case because Bell refused to follow their recommendations -- sought to indict Ingram on a false-statement charge, sources have said, because he lied to the General Accounting Office about a break-in in late 1974 -- long after the bureau said such entries had stopped.

In his report to Civiletti, Webster said "it may reasonably be concluded that there was a deliberate attempt to withhold the existence of surreptitous entries from the GAO auditors in this one instance."