Rob Wilson was responding to a question in the House of Commons by Sir Edward Leigh, who raised concerns over whether so called British values would trump religious values and prevent groups from teaching their own faith.
In his response, the Minister said: "More than 25,000 registered charities involve the promotion of religion. They play a hugely important role in our communities and support those in need.
"I pay tribute to their excellent work. They are often first in and last out of some of our toughest communities."
The issue was raised following a decision by the Charity Commission to remove the charitable status of a group linked to the Plymouth Brethren.
The Commission deemed it wasn't working in the interest of the public, however the decision was later overturned.
It led to some feeling Christian groups could be targeted in future for bringing their faith into their charitable work.
Mr Wilson said: "My hon. Friend will know that the Charity Commission is independent of the Government and the Cabinet Office.
"It already respects the diversity of religious views, registering hundreds of new religious charities from a range of faiths every year, but it is fair to say that the Charity Commission did need to improve, as the National Audit Office said.
"It is now well on its way to doing that, but he can be assured that the Charity Commission has learnt its lessons from the case he raises."