"The problem of Islamist extremism and charities ... Is not the most widespread problem we face in terms of abuse of charities, but is potentially the most deadly. And it is, alas, growing," William Shawcross, who took on the role at the Charity Commission in 2012, said.
"I'm sure that in places like Syria and Somalia it is very, very difficult for agencies always to know what the end use of their aid is, but they've got to be particularly vigilant," he said.
The regulator is currently investigating a number of charities raising funds for causes in Syria.
He said he has written to Prime Minister Cameron to ask for changes to the law.
British security services have been tracking Britons travelling to Syria for several years and, with concern growing, are now devoting more resources to this. There have been only a handful of arrests so far; the most serious relates to an alleged plot, while others are for allegedly attending training camps in Syria.
But he said the Charity Commission needed better funding and stronger legal powers to improve.
"We need two things if we're to continue to improve the commission's performance," said the biographer and author.
"We need a more sustainable funding position and we need stronger legal powers to tackle abuse and mismanagement.
"I know public finances are tight but our funding situation is unsustainable.
"We cannot keep responding to continuous salami-slicing of our budget," he said.
