The risk from terrorism and extremism was "one of the most deadly threats faced by some charities today," said William Shawcross, chairman of the Charity Commission.
"The crisis in Syria has evoked a generous public response, but with this comes a greater risk of charities being subjected to abuse," the Telegraph quoted him as saying.
It said that some aid workers who travelled to Syria and Iraq have been recruited by terrorist groups, while other charities have seen their goods stolen and staff kidnapped.
Latest figures show that the commission, which regulates the operation of charities in the UK, has seen a significant increase in the number of serious incidents and reports about charities being targeted by extremists and terrorists in the past year, the paper said.
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"The number of formal legal disclosures of information between the commission and the police and other agencies over charities caught up in alleged Islamist activities more than doubled between 2014 and 2015," it said.
"We are opening more investigations and using more of our powers to regulate charities effectively," Shawcross said.
"We are working hard, together with other agencies, to prevent Islamist abuse of charities and to counter any terrorist threats," he added.
Over 50 formal investigations and assessments conducted by the watchdog during 2014-15 involved concerns about the abuse of charities for terrorist or extremist purposes.