The Office of the Third Sector last month sent formal grant offers to 32 organisations for the programme, which was set up to strengthen the ability of small charities to campaign.
But third sector minister Angela Smith suddenly scrapped the scheme this month, saying the money was being diverted to the £16.7m Hardship Fund. The decision was taken without consultation and thus in breach of the Compact, which outlines how the public and voluntary sectors should behave towards each other.
Willott said the decision was shameful.
"What is so appalling is the manner in which this has been done, with no warning or consultation," she said. "How does the Government expect to convince other public bodies to abide by the Compact when they treat charities in this way?"
The EDM calls on the Government to reinstate the funding for the programme "without delay".
EDMs are formal motions submitted for debate in the House of Commons, but they rarely get debated and are regarded primarily as a way of raising awareness of an issue.