John Reid was accused of misleading the public after it was claimed that five illegal workers had been cleaning Immigration Service offices for years.
The group of Nigerians was detained on Thursday after being sent to the London offices of the Immigration and Nationality Directorate by a cleaning company, Techclean.
Mr Reid insisted they had been stopped at the gates before they could start work - and said it proved the system was working. But his version of events was contradicted by the Surrey-based company that supplied the five cleaners.
In a statement to Channel 4 News it said: "Each of the five individuals has worked at the premises of the IND on a number of occasions, one of them for about three years."
The programme reported that two of the men had been working at the IND for two years, one man for one year and one for six months.
After the initial claims Mr Reid gave a series of interviews in which he praised the "alertness" of the security staff that apprehended the cleaners.
He said: "Like all good employers, we check the credentials of everybody who works in our buildings and those who work for our contractors. When a group of people turned up who had not been cleared our security people there immediately noticed this, called in the authorities and they were arrested, I don't think that's a sign of chaos."
David Davis, the shadow Home Secretary, launched a fierce attack on Mr Reid last night. "Yet again we see the Home Office, and now the Home Secretary, have misled the public over a very serious breach of national and Home Office security."
A Home Office spokesman promised last night to investigate the new allegations "fully and as quickly as possible". The spokesman said: "[Mr Reid] made it absolutely clear that no system was 100 per cent foolproof and that there may have been occasions in the past where people had got through the system."
Techclean told Channel 4 News that all five of the men had been through the company's normal checking process. Four had had their passports and national insurance documents checked and had visa entry details. The fifth had a letter from the Immigration Service confirming his right to work in the UK.
Mr Reid is desperately trying to draw a line under the crisis that has paralysed the department since the admission last month that 1,023 foreign prisoners had been released without deportation hearings. But the bad headlines have continued in recent days.
A senior IND official has admitted that he did not have the "faintest idea" how many illegal immigrants were in Britain.