The Charity Commission investigated 16 allegations of links between charities and terrorism in 2008/09, according to the regulator's second annual Charities Back On Track report.
The report, which summarises the main themes from the commission's recent compliance work, says the cases reinforce the regulator's view that the best way for charities to limit the risk of terrorist links is through robust financial, governance and management procedures.
Inappropriate political activity has been another major source of concern for the commission. It investigated five such cases in 2008/09, including the high-profile Smith Institute case. Last week it also opened an investigation into the relationship between Atlantic Bridge and the Conservative Party.
Other common themes have included poor financial mismanagement, the failure to safeguard vulnerable beneficiaries and various trustee and governance issues such as unsuitable trustees and inadequate oversight and controls.
The report reveals that the commission carried out just over 1,500 assessments of concerns about charities raised by the public and others in 2008/09 and directly protected £47m in charitable assets. Of 255 reports of serious incidents, 142 involved fraud, theft, misappropriation or significant loss of funds, and 37 involved allegations of abuse of vulnerable beneficiaries.
The average duration of statutory inquiries fell from 414 days in 2007/08 to 358 in 2008/09; and the number of inquiry reports published fell from 42 to 23. But instances in which the commission used its statutory powers increased from 490 to 707.
The report also notes that the commission put an unnamed London charity's £1.5m premises in the hands of the Official Custodian for Charities amid a dispute over the identity of valid trustees and concerns that the building had been bought to form a breakaway charity.
The OCC holds property on behalf of charities and the commission has to consent to any sale.