Part of the Strengthening Families grant programme from the Department for Education and Skills has been delayed by more than a month, leaving a number of charities in the lurch.
The programme's development grants have not been announced, despite the application form stating that charities would be told whether they were successful before the end of March.
Marriage Care, a charity that has received government funding for 10 years for its work offering support and advice on marriage and family relationships, is among those waiting to hear.
It has applied for money to set up a project to develop emotional literacy programmes in primary schools.
Chief executive of the charity Terry Prendergast said: "We stick to our application deadlines, but the Government gets flaky about its end of the deal."
A statement on the grants programme website apologised and said ministers wanted more time. It added that applicants would be informed "as soon as we are able".
Prendergast said: "It is problematic for charities that we have to hang around, but if the ministers are considering it in more depth, at least they are giving it the time it needs."
The head of public policy at Relate, Cheryl Turner, said that although the charity had been told it would receive a strategic grant, it was still waiting for the money. She said: "We are finding it uncomfortable."