John Reid has accused his opponents of "playing politics" over reports the Home Office ignored files on Britons who committed crimes overseas.
Mr Reid has said he is taking the problem "very seriously"
Mr Reid said he was unaware of 27,500 files not entered on a police database, which has prompted fears some may have been cleared to work with children.
He is facing growing opposition calls to publish a letter from last October showing how much was known.
Mr Reid has promised an inquiry but insisted the problem was being fixed.
In an interview with BBC Radio Nottingham, Mr Reid said officials were trying to make sure that anybody who might have "slipped through the net some time ago" was discovered.
"If anybody wants to play politics with it, let them do it," he said.
"My job is to give public protection, that's what I'm doing."
Of the 540 most serious cases, which include rapes, murders and paedophilia, 260 have now been entered onto the police national computer.
Mr Reid has said another 280 cannot be entered yet, because there were not enough details.
SOME OF THE CASES
3 attempted rapes
17 other sex offenders
9 attempted murders
The Association of Chief Police Officers (Acpo) said that before it took over responsibility for the data in March 2006, details of 27,529 cases had been left in Home Office files.
The Home Office said ministers had been unaware of the scale of the backlog until this week.
But a letter, written last October, apparently warned the Home Office that police were having problems tracing hundreds of British criminals convicted overseas - although Acpo says it did not mention the backlog.
Now the Conservatives and Liberal Democrats want the letter published - a demand so far resisted by Mr Reid.
Lord Chancellor Lord Falconer also faced repeated calls, on Thursday's edition of BBC One's Question Time, for the letter to be published .
"You're in charge of the criminal justice system. What is the argument against publishing the letter now?" shadow chancellor George Osborne asked Lord Falconer.
Lord Falconer replied that "there should be an inquiry".
Shadow home secretary David Davis said the position of ministers Tony McNulty and Joan Ryan, who replied to the letter, would be "untenable" if they had known of the problems with the offenders' details.
Mr McNulty told BBC Radio 4's Any Questions that he had been sent the Acpo letter in October but had seen it only two days ago following Acpo's public acknowledgement of its existence.
He said: "It was passed, as is totally normal if it's not someone's area, on to (Joan Ryan, minister responsible for the Criminal Record Bureau), who answered and answered it in an entirely appropriate fashion."
Mr McNulty said he was happy for the letter to be published but only after an inquiry had been completed - a position ridiculed by the opposition.
It has been suggested the letter said the home secretary should be appraised of the situation, but Ms Ryan has said she had decided not to.
Mr Davis has written to the Foreign Office to clarify whether or not they hold the information needed to identify Britons who have committed crimes abroad.
It comes after ministers said the Home Office could not enter details of some offenders on to the police database because information received from other countries had been incomplete.
Asked whether he could say for sure that files containing details of offences committed by Britons abroad might still reside in boxes in the Home Office, Mr McNulty said: ''I can't, no, to be perfectly frank.
"I apologise for the failures that there have been in terms of ministers not knowing about the backlog. I think that's right, and [it] should not have happened in public policy terms."