Clark said third sector minister Ed Miliband and his superior Hilary Armstrong, the Chancellor of the Duchy of Lancaster, should have solved the problem when their offices first learnt of it in November.
Instead, CSV had to resort to exposing the department in the media in December to get a commitment that the money would be paid.
The Office of the Third Sector "should have had the clout to bang Whitehall heads together", Clark said. "Despite the intervention of both Ed Miliband and his boss Hilary Armstrong, the DoH still held on to the money it owed."
Miliband admitted to the House of Commons last week that the CSV incident was a bad case. He said: "My right honourable friend the Chancellor of the Duchy of Lancaster and I got involved to expedite the process."
The grant has now been paid, but CSV has invoiced the DoH for the interest on the money. It would not reveal the total claim, but it is believed to be about £3,000 a week.
A DoH spokesman said: "The Treasury is in discussions with CSV about any additional costs it might have incurred as a consequence of the delay and will look at any claims for compensation in light of these discussions."