It will take "years not months" to get the immigration service working the way it should, its boss has told MPs.
Ms Homer said there had not been enough staff to deal with the cases
Lin Homer, Immigration and Nationality Directorate chief, spoke as the Home Office was given six weeks to draw up a plan to make it "fit for purpose".
She told the Commons home affairs committee it would take "at least a couple of years" to get the service "into the shape I would like".
She felt she had "let down" the axed Home Secretary Charles Clarke.
She said several hundred of the foreign criminals facing potential deportation have been allowed to stay in Britain.
She also confirmed eight serious sex offenders released without being considered for deportation were still at large.
For the Conservatives, shadow home secretary David Davis said this showed the government had failed to get a grip of the crisis at the Home Office.
"The fact that the Home Office has already decided not to deport 200 foreign criminals gives lie to the prime minister's promise to 'automatically deport' such criminals.
"This all demonstrates that the Home Office still has not got control of this scandal."
Nick Clegg, for the Liberal Democrats, said: "Ms Homer's evidence shows that Labour's tough talk on fixing the immigration service is nothing but hot air.
"John Reid's pledge to turn around the Home Office in six weeks and Tony Blair's vow to deport all foreign prisoners have been exposed as unworkable."
But Mr Blair said while there had been "real progress" in sorting out asylum, the immigration department was still not working properly.
He said Ms Homer was doing a "fantastic job" in difficult and constantly changing circumstances.
Ms Homer was giving evidence to the influential cross-party committee about immigration control.
Her department has been in the spotlight for weeks following the release of 1,019 foreign prisoners without consideration for deportation, and a succession of other failings.
Ms Homer told MPs there had not been a deliberate plan to let the foreign prisoners go - busy staff had simply filed the cases away when there were not enough workers to take them on.
But staff had since been drafted in from other parts of the IND, including managed migration and asylum, to deal with the problem, she said.
"I think we are struggling to get absolutely the right balance in terms of resources and skills in the criminal case work team immediately... not least because we are dealing with intense circumstances," she said.
It was not just a question of numbers - staff had to be properly trained too, she said.
There was also a concern that the areas they were being transferred from would suffer as a result and that she could be "swapping one backlog for another".
Asked by MPs whether senior figures in the Home Office had supported ex-home secretary Mr Clarke, she told MPs: "I felt I let him down."
Two weeks ago the new Home Secretary, John Reid, had to apologise to the committee after he discovered that a foreign murder he had claimed was in jail had in fact been released on bail.
Two senior officials were removed from their duties after it emerged the home secretary had not been told that bail hearings were taking place.
The Home Office opposed bail but lost in a number of cases.
The committee's Labour chairman John Denham asked Ms Homer why nobody had thought to tell her about the hearings.
She said she was carrying out an investigation into this but admitted she had "a lot of work to do".
Pressed about how many cases the Home Office had lost in the past fortnight, she said she was unable to give the committee the latest figures.
But she said there were three or four bail hearings each day.
She told the MPs that no more murderers had been released, but suggested that another serious offender had applied successfully for bail.
Asked by Mr Denham about press reports that six IND staff had been sacked for selling visas, Ms Homer replied that she "did not recognise that number".
But she added: "At any time we are undertaking a number of investigations into potentially corrupt behaviour by members of staff.
"In the last full year that I have figures for, that activity led to 15 members of staff being either dismissed and/or prosecuted. So I would have more confidence in that than the figure that has been quoted to you."
A Home Office spokesman later confirmed those figures.
"Since January 2005, 15 members of Immigration and Nationality staff have been dismissed following investigations by our security and anti-corruption unit over allegations of professional misconduct," he said.
He refused to release figures for previous years and said he could not confirm whether the 2005 figure included the individuals accused of selling visas in weekend press reports.