By Jon Silverman
Legal affairs analyst
Not since the spectacular jail escapes of the early 1990s has a home secretary found himself under such pressure over failings in the prison service.
Prison issues are causing fresh problems for Mr Clarke
And the timing could hardly be more embarrassing for Charles Clarke and his ministers.
Following a series of murders by recently released prisoners, the Home Office is struggling to regain the initiative on violent offenders.
The admission that it has "lost" over 900 foreign nationals who were in the prison system is another major setback.
At the root of the problem is the unprecedented rise in the number of foreign nationals in the prison system of England and Wales.
In February 2006, there were 10,265 of them, representing 13% of the prison population.
The prison service has been unable to keep pace with the administrative implications of such a rise.
Indeed, some foreign nationals are held well beyond the end of their sentence because their cases have been lost in the system or because of deportation delays.
The Prison Reform Trust has examined the problem and its director, Juliet Lyon, accused the Home Office of failing to develop a coherent strategy for foreign national prisoners.
For immigration barrister, Simon Harding, the blame lies with both the prison service and Immigration and Nationality Directorate (IND).
"The asylum system has been shambolic for many years," he said.
"And it is down to administrative incompetence that people recommended for deportation have not been arrested at the prison gate on release."
It should be pointed out, however, that some of the most serious offenders may be under probation supervision so they have not disappeared entirely.
There are two means by which foreign nationals who commit crime may be deported.
One happens at the point of trial, if the Crown Prosecution Service can persuade the judge to make such an order when passing sentence.
The other is if the Home Office itself applies for such an order no earlier than 12 months before the end of sentence.
Foreign nationals who commit serious crimes can be arrested under immigration law upon release.
If considered violent, they are likely to be held in a detention centre to await a hearing.
According to the Home Office, in 160 of the current cases, the courts had recommended that deportation should be considered on release.
Only 14 of these had been identified. This implies a complete breakdown in communication and record-keeping between the prison service and the IND, which is very worrying.
There is some irony in a call by Mr Clarke's predecessor, David Blunkett that "heads should roll".
It was Mr Blunkett, in a flourish of publicity, who announced in 2003 that asylum seekers who committed serious offences in Britain would face deportation.
It now emerges that Mr Blunkett was also presiding over a system which was incompetent and incapable of making good his pledge.