Jacqui Smith is learning the oldest rule about being Home Secretary: there are unknown difficulties buried in the basement of the Home Office with a toxicity to damage and even destroy political careers.

Sent into the Home Office to bring a less frenetic tone than her predecessor John Reid, Ms Smith was told within three weeks of becoming the first female Home Secretary that thousands of illegal migrants had been cleared to work as security guards.

The new Home Secretary had two choices: either come clean immediately about the problem or keep quiet until officials had worked out the extent of the latest immigration fiasco to hit the department.

Ms Smith was dammed if she did, and dammed if she didn’t. Within the Home Office memories were still fresh of the way Charles Clarke handled the issue of foreign national prisoners freed from prison without being considered for deportation.

Mr Clarke chose openness. He disclosed the emerging problem, but was unable to provide exact details of how many people were involved with the result that the roof fell in and his Cabinet career was ended.

That experience scarred the Home Office and dominated thinking and advice given to the new Home Secretary. Better to marshal the facts before going public seems to have been the guidance offered to Ms Smith.

But another factor was also clearly at work. The splitting of the department into a terror-focused Home Office and separate Ministry of Justice has been seen among senior Home Office officials as a new beginning, an attempt to rid the Home Office of its reputation for poor management, crisis and blunders.

The Home Office has become obsessed with its reputation and Ms Smith was warned that if the press discovered the Security Industry Authority had issued licence to illegal workers "there will be significant criticism of the Home Office and our processes. They are likely to refer back to other Home Office so called ‘blunders’ which adversely affected coverage of the department last year and earlier this".

Ms Smith chose to keep quiet but the risk was always that the there would be a leak – as has happened – resulting in her emergency statement to the Commons this afternoon.

The Department – indeed the Government as a whole — remains hyper-sensitive about the issue of foreign nationals, immigration and illegal working. Only a few weeks ago, it deliberately did not publicly announce that the a package of support for foreign national prisoners was being almost doubled to £1,500.

The information was leaked to The Times and the Home Office explanation for not formally announcing the new figure was that it was simply a time-limited enhancement of an existing scheme.

So the Department, despite the new broom at the top, has form on wanting to keep damaging or potentially damaging news out of the media.

Despite the embarrassment, Ms Smith argued correctly this afternoon that it was the "legal duty" of employers and not the Security Industry Authority, which licenses private security guards, to check whether employees are eligible to work in the UK.

The Security Industry Authority started work in 2004, issuing 250,000 licences including 40,000 since March 2006 for security men and women guarding buildings. The SIA checks an applicants identity, training and criminal records, but not a person’s right to work in the UK.

Since July when the problem emerged, the SIA has been checking an applicant’s right to work and currently are working through the 40,000 licences issued since March 2006. It is estimated that 5,000 people without the right to work in the UK have been issued with a licence.

Times Recommends

• Should Knox’s trial even have reached the courtroom?
• All that glitters is not sold in Wright’s world
• Believe it or not, Big Brother is your friend