Approaching half of the programmes, 19, also failed to provide the recommended minimum three-year funding, the report said.
“The approach to covering overheads, full costs and core costs and providing full cost recovery was inconsistent and unclear across and within departments,” the report said.
Making applications and assessing progress in this area was “very difficult”, it concluded, because of “unhelpful guidance and unclear language” in many cases.
The commission also said that the study was retrospective, and it recognised that progress had been made in tackling some of the issues, including the Government’s pledge to make three-year funding the norm.
A spokesman for the Cabinet Office admitted there was work to be done but said the Government was taking action.
“We know that the language of the Compact can be confusing, which is why the third sector review calls for a need to bring the Compact and its codes fully up to date,” he said.
He added that the Cabinet Office would be working with the Commission for the Compact to ensure a “more thorough implementation” of the agreement.