Revd Nadim Nassar made the comments on Premier's News Hour as nine Britons arrested for trying to cross illegally from Turkey into Syria are expected to be deported today.
It was not clear why they were trying to cross the border.
The planned deportation comes as a new UN report says more than 25,000 foreign fighters have travelled to join groups like Islamic State.
The fighters, from more than 100 countries, have travelled to areas including Iraq, Syria, Afghanistan, Libya and the Philippines.
The report said its analysis indicates that the number of foreign terrorist fighters worldwide increased by 71% between mid-2014 and March 2015.
UK security services alone estimate 600 Britons have gone to Syria or Iraq to join militant groups.
Revd Nassar, director, Awareness Foundation, a charity which works to promote relationships between different faiths, has accused some Muslim leaders in Britain of having the wrong attitude towards tackling the issue on home soil, he said: "Extremism is out of control in Britain.
"Still some Muslim institutions are not challenged enough about how they are running their affairs. When we challenge fanaticism the Muslims should thank us, if the Muslims are feeling offended there is something wrong in their attitude, not in how the Government is treating fanaticism."
Revd Nadim Nassar:
