In his letter, Eric Pickles said there is "more work to do" in rooting out militancy.
He also said, "there is a need to lay out more clearly than ever before what being a British Muslim means today: proud of your faith and proud of your country."
Mr Pickles went on to say, "we know that acts of extremism are not representative of Islam; but we need to show what is."
Some leading clerics have criticised Mr Pickles' letter, as it implies Islam is naturally separate from and opposed to British society.
Julian Bond, the Director of the Christian Muslim Forum, told Premier's News Hour: "What we've seen over the last week and more is many, many responses from individual Muslim leaders and Muslim organisations condemning violence, terrorism and killing.
"So much work is being done, and the importance message is that at the heart of Islam is the condemnation of extremism.
"So the Quran itself talks about being moderate and following the middle way.
"People are becoming radicalised outside the mainstream - it's not through things that they've heard in the mosque.
"And what we have heard on a number of occasions with previous bombers and would-be terrorists, is that they were thrown out of the mosques.
"The mosques have done so much, and that needs to be recognised.
"They [the general public] will pick up things like this letter which is saying that the Muslim community and imams need to do more to condemn things that they're already condemning."
Prime Minister David Cameron has publicly defended the letter sent by his Communities Secretary. He said: "It's absolutely right to write this letter.
"Anyone who reads this letter - and I've read the letter - will see that what he is saying is that British Muslims make a great contribution to our country, that what is happening in terms of extremist terror has nothing to do with the true religion of Islam - it's being perverted by a minority who have been radicalised.
"But everyone needs to help with dealing with this problem of radicalisation.
"And anyone frankly reading this letter who has a problem with it, I think really has a problem, because I think it's the most reasonable, sensible, moderate letter that Eric could possibly have written."