Stoker made the admission last week when he was called to give written and oral evidence to the public administration select committee, which is conducting an enquiry into the third sector's role in public services.
When pressed by Tony Wright MP, the committee chairman, to clarify whether or not charities receive different terms under Compact-compliant contracts, Stoker confessed: "If the Compact was delivered, charities would be treated in some ways differently."
The Compact includes clauses that give special consideration to black, minority and ethnic groups, and to community groups, Stoker explained. It also commits government funders to holding "meaningful and timely" consultations with voluntary organisations. "The measures don't exist in the same way for other sectors," Stoker said.
In his written evidence to the committee, Stoker said: "On a level playing field it may not be straightforward for commissioners to deliver consistently and fully the Compact financial undertakings to third sector partners unless these have been built into the terms of the programme concerned at the outset, and thus apply to bidders from other sectors too."
Wright said Stoker's evidence was "potentially explosive".
Stoker also hardened his position on how charities should approach relationships with statutory bodies. He said: "My first instinct would always be to make the challenge and call the bluff."