Brown named the abuse of charities as one of the most dangerous sources of terrorist finance, in a speech to the Chatham House think tank last Tuesday.
"We know that many charities and donors have been and are being exploited by terrorists," he said. "It is important to look at the whole sector so that dubious charities are rooted out and good charities protected from abuse."
But Kenneth Dibble, director of legal and charity services at the commission, said it would look only at those charities that operated in areas or ways that could pose a risk.
He said: "We don't want to be invasive where we don't need to be." He added that the commission would avoid singling out certain types of organisations, such as faith groups.
The Charity Commission has opened two investigations into alleged terrorist abuse of charities this year.
It has also been working with the Home Office and the Treasury on a review of how charities can be protected from financial abuse by terrorists.
The results of the review will be reported later this year, but Dibble admitted he did not know what the Government would decide. "There may be a bigger picture that the Treasury sees but we don't," he said.
Sector commentators branded the review impractical when it was announced in June (Third Sector, 21 June), and Brown's comments added fuel to the fire.
"He's taking a very cautious position in order to deal with what must be a tiny problem at most," said Peter Cardy, chief executive of Macmillan Cancer Support.