In his evidence to the Public Administration Select Committee, Clark expressed concern over the way in which the Office of the Third Sector announced in the third sector review last year that the commission would be reviewing its CC9 guidance on campaigning. The review said the Government would "work with the Charity Commission to change this guidance".
At the hearing, Clark said: "I think this raises interesting questions about the role of the commission."
Speaking to Third Sector after the meeting, he added: "I was a little surprised by the language the OTS chose to use about an independent regulator on a politically sensitive issue.
"It would be wrong to suggest that the commission is under the thumb of the Government. I am not implying that there is a huge issue of independence that I am aware of. I think the commission was under pressure from the advisory group, which had been encouraged by the Government. The commission was possibly a bit too eager to revise the guidelines."
The committee, chaired by Tony Wright, Labour MP for Cannock Chase, held the one-off meeting last week to discuss the new guidelines on campaigning and political activity, published last month. Advisory group members Ian Leggett, director of student campaigning charity People and Planet, and Brian Lamb, director of communications at the RNID, also gave evidence. The commission did not.
Speaking after the meeting, Leggett said the group was not working with the Government. "We set up the group because there were lots of people in the sector who thought the guidelines were unclear," he said.
"We chose Helena Kennedy as our chair and we didn't even inform the OTS what we were doing. Ed Miliband made a couple of speeches in which he recognised the positive role of campaigning organisations, but it wasn't encouragement in the practical sense."
A spokeswoman for the Charity Commission said: "The commission has been very clear about the reasons for revising our campaigning guidance. In rewriting our guidance, we are responding to calls from the charitable sector to clarify the language used in the existing guidance so that trustees are more confident about the extent of political activity they can engage in under charity law."