Tessa Jowell, Secretary of State for Culture, Media and Sport, claimed the decision to bring together the two bodies was based on widespread consultation.
But the Government's own consultation document states the response to merger proposals was anything but positive with the voluntary sector, local authorities, lottery distributors and even the Government all expressing hostility.
John Whittingdale, Conservative shadow spokesman on Culture, Media and Sport, plans to raise the issue in Parliament. He said: "The fact that the Government appears determined to press ahead with the merger in the face of opposition from almost all those that responded to the consultation will further increase suspicion that this is a takeover bid by it to gain political control of the Community Fund and to undermine its independence."
A summary of responses published on the Department for Culture, Media and Sport's web site states: "The vast majority of respondents from the voluntary sector felt that reducing the number or merging some of the distributors would be a mistake.
"The general consensus was that it would cause huge disruption, not only to the expertise gained but also to the applicants as well as the processing of applications."
Jowell, in contrast, said on 28 February: "The decision to merge the Community Fund and the New Opportunities Fund arose directly from that consultation and the messages we received from it ... We have carefully considered the responses received from the voluntary sector about the merger."
The consultation began in July before the Daily Mail launched its campaign for the Community Fund to be abolished following the controversial grants to asylum seeker groups. It even reveals opposition among Jowell's colleagues to the merger. Under the heading "Government and MPs", the summary of responses states: "There was no support for reducing or merging the number of distributors as they thought it would result in a loss of expertise as well as being costly to implement."
Jowell has subsequently claimed of the merger: "The notion that it is in any way related to the recent controversy over the grants is without foundation."
Stephen Bubb, chief executive of ACEVO, said that the consultation results "put in context the promise to consult on the merger because they must have known there was no support for it".
Bubb said he would discuss issuing a joint referral with Stuart Etherington, chief executive of NCVO, to the Compact Working Group to determine whether the Government had broken Compact guidelines on consultation. "A fait accompli is not consultation," he said.
A spokesman for the Department for Culture, Media and Sport said: "The Government is making a decision on this and we feel it will make the distributors less bureaucratic and more efficient."