Palmer sits on the board of a company called Charity Business, which has created a software tool to help charities report their expenses.
The NCVO published a statement yesterday confirming Palmer had resigned, but a spokeswoman declined to say why. She said the group, which was set up because of concerns about the transparency of expenses claims, had replaced him with two people - John Stoker and Peter Grant.
Stoker was the first Commissioner for the Compact from 2006 to 2008 and was chief commissioner at the Charity Commission from 1999 to 2005.
Grant has developed a masters-level programme in grantmaking and philanthropy at Cass Business School.
The expenses panel is expected to publish its guidance for the sector at the end of the year.
Third Sector is seeking comment from Palmer.