Chief executive Sylvia Brown said the decision had been made partly because of Acre's stretched resources, but was also due to concerns at Acre about how useful the hubs would be to its members.
Brown said: "We represent very small community organisations with no paid staff. We disagree with the structure of ChangeUp in that we don't think small organisations really see governance and performance improvement strategies as separate things."
Brown said the governance hub had tried to adapt its structure to be relevant to small community groups but that there was still too much duplication among the six hubs, each of which is developing its own website and materials.
She said: "If you're on the committee of a village hall, you don't want to have to search half a dozen separate websites and toolkits."
Mike Hudson, interim chair of the governance hub, said he understood that the Acre representative had found it difficult to attend hub meetings because of resource problems and because Acre is not based in London.
But he added that Acre was "not leaving in a huff" and would remain involved at some level.
Other partners on the governance hub, which is based at the NCVO, include Acevo, Charity Trustee Networks and Volunteering England. This week, it has published a new governance code for the sector that aims to increase the impact of charities and boost public trust.