To combat the threat, the commission is to set up a specialist counter-terrorism team and create a new monitoring service that will be led by intelligence supplied by law-enforcement agencies. The regulator insists no such agencies will be based within its offices.
The warning follows the Treasury's introduction last week of tougher money laundering regulations to prevent terrorist financing through firms of lawyers, accountants, casinos and estate agents. It is part of the commission's response to the joint Home Office and Treasury consultation on charities and terrorism, which closes tomorrow.
Other pledges include work to identify risk areas and provide new best practice guidance for the sector. The commission will also run an outreach programme to raise awareness of legal requirements and arrange training in financial investigation for its staff. This will be paid for by £1m of extra funding that was awarded by the Treasury in March.
The response of the commission outlines areas of particular difficulty, such as potential damage to the credibility of faith groups.
"We consistently emphasise the value of the work faith-based charities do and will continue to do so," said David Walker, development manager at the commission.
"We hope that by consistently reiterating the dangers, all agencies involved in minimising this kind of abuse will ensure they do not make assumptions about links between terrorist exploitation and faith-based charities."
Walker added that the commission would strive to maintain independence despite the changes. He said: "We have worked closely with a number of law enforcement, intelligence and government agencies for some time and have always been clear about our independent role. This is vital for our credibility and the credibility of other agencies, as well as the sector we regulate - we have no intention of compromising this."