The NCVO's Compact advocacy programme has taken up 16 cases against the department since 2003. The Department for Education and Skills is the next biggest offender, with 11 cases.
"The Government agreed to the Compact almost 10 years ago," said Saskia Daggett, Compact advocacy manager at the NCVO. "However, too often, government is not playing by the rules. Voluntary organisations are suffering as a result."
The Government introduced the Compact to improve relations between the voluntary and public sectors. However, the figures suggest many departments do not practise what they are supposed to preach, and plans to get charities to deliver more services could be jeopardised unless they improve. Charities have walked away from contracts with the Learning and Skills Council, which is funded by the Department for Education and Skills, because they were too high-risk and paid in arrears.
"Complaints about Jobcentre Plus include failing to fund the full cost of work, paying in arrears and not explaining the risks of contracts properly," said Daggett. She urged departments to follow the "great steps" made by the Department of Health.
The NCVO has taken on 72 cases against government departments and agencies since 2003. Its targets include the Legal Services Commission, for running consultations as short as six weeks, and the Department for Transport, for denying repayment of full costs.
A DWP spokesman said: "We've offered to meet the NCVO to discuss its concerns, and we are reviewing our funding arrangements, in part with enhanced risk-sharing in mind. We do pay in advance if the case for doing so is made.
"Jobcentre Plus has introduced a specific requirement for prime contractors to produce signed evidence that all their subcontractors understand and agree the payment arrangements. This gives third sector organisations a firm basis for negotiation."