Home Secretary John Reid is to look into claims that a leading member of a radical Islamic group is working as a senior official at the Home Office.
John Reid said officials would investigate the BBC claims
A BBC investigation revealed that Abid Javaid works for the Immigration and Nationality Directorate, in Croydon, south London.
Mr Javaid is also a member of the Muslim group in question, Hizb ut-Tahrir.
Prime Minister Tony Blair has called for the banning of the group.
Mr Javaid's involvement with the group was unveiled during a joint investigation by Newsnight and File on 4 into the radicalisation of young Muslims.
The probe - screened on Tuesday - also found that banned cleric Omar Bakri Mohammed was preaching support for terrorism by appearing incognito on the internet.
Mr Javaid works at Lunar House where thousands of visa and asylum claims are processed each year.
When approached by BBC investigators he admitted being involved with Hizb ut-Tahrir, or HT, but denied he was a leader.
An elder at Croydon Mosque, which has been trying to get rid of radical elements, told the programme Mr Javaid had represented HT at meetings. Shoib Minhas said: "One day he gave me his card. An introductory card. It had a contact number on it and it showed he worked in the Home Office.
"He also mentioned himself he worked in the Home Office."
Tony Blair said last August that HT would be banned but so far the group has remained off the list of proscribed groups.
A Newsnight investigation in 2003 discovered that its website promoted racism and anti-Semitic hatred, called suicide bombers martyrs, and urged Muslims to kill Jewish people.
In Denmark, HT's spokesman has been found guilty of distributing racist propaganda.
The group is banned in some countries.
Germany and Russia are among the countries in which it is illegal, while it has also been officially targeted by Central Asian states such as Uzbekistan.
HT said in a statement on Wednesday it was a non-violent Islamic political group.
"We are a non-violent organisation that has worked for over 10 years in Britain," the statement said.
"For the avoidance of any doubt we do not advocate or otherwise promote the use of violence or any criminal activity against civilians in the UK or anywhere else in the world."
An HT spokesman denied the organisation was anti-semitic. He said the accusation had arisen because of its opposition to the state of Israel.
"We defend the right of people living under military occupation to defend their land with the proviso that they do not kill innocent civilians," said Taji Mustafa of HT.
Mr Mustafa said HT adovocated an Islamic state across the Middle East that would respect other people's beliefs.
The Tories described Mr Javaid's employment in the Home Office as "appalling".
Patrick Mercer, the party's homeland security spokesman, said: "To think that there is a senior radical at work inside the Home Office in a very, very sensitive area is appalling."
Mr Reid said on Wednesday he had told officials to look into the evidence unearthed by the BBC.
He said: "Unfortunately, I've not only got to protect the country, but to protect our laws and liberties.
"If there is evidence, then the BBC no doubt will let us have it, and I instructed my officials last night to ask for such evidence.
"If there has been a breach of the code of conduct or the civil service code by an employee, that will be dealt with, and dealt with robustly."