Charities with an annual income of between ?£250,000 and £10 million are now liable to receive a call from the Charity Commission under a review visits programme beginning next month.
Of the 9,000 charities that fall into this category, 600 will be visited each year by Commission staff and interviewed for between three to six hours.
"The Commission is getting more involved in governance and these visits will be considerably more intrusive than in the past,
said Simon Gillespie, the Commission's director of operations.
"We want to get senior employees and trustees together and look at the interaction between them."
Charities working in high-risk areas such as international aid or war zones plus those with suspected terrorist links are most likely to be visited. Those that fail to submit annual accounts or leave poor auditing trails can also expect a call.
Gillespie said the Commission understood the difficulties faced by organisations working in emergency situations but they could not ignore the governance issues surrounding international aid agencies working overseas.
"The joint UNHCR and Save the Children-leaked report recently claimed that aid workers had abused children in West Africa. This area needs work,
Several charities have already requested visits, which will be carried out by the Commission's charity support arm rather than the investigations team.
But according to Ian Brown, a campaigner for the reform of international charities, the proposals do not go far enough. "Going to the headquarters is a waste of time. Unless they go out into the field, it's not going to be effective. Fraud and malpractice can be hidden by many large organisations working in several different countries."