Wirral CVS wrote to the shadow board of the new organisation, Voluntary and Community Action Wirral, to say that it was pulling out, but did not give a reason.
Wirral CVS is understood to be unhappy about the way the process has been managed.
Viv Kenwright, co-acting chief officer, told Third Sector: "We have withdrawn from the current process, but we are still positive about the merger."
Annette Roberts, chief executive of VCAW, said the remaining four organisations were proceeding with the process, but the door was still open to Wirral CVS.
The merged organisation is expected to be launched in April 2008.