The report states that the government's political agenda, dealing with issues such as public disquiet asylum seekers and refugees, can result in inadequate consultation with charities and local organisations, which may suffer as a result.
"The Government often consults when it suits them, but it can quickly change tack when a higher political priority is involved," said Richard Hebditch, research officer at the Compact Advisory Programme.
A spokesman at The Refugee Council said it was recently given seven working days to respond to proposed changes to refugees' rights to travel documents, instead of the 12 weeks stipulated in the Compact's consultation guidelines.
"It's difficult to see how we could effectively respond in such a short period of time, especially when the proposed changes would have a huge effect on our service users and the charity itself," he said. "We have a pretty good relationship with Government, but this is not as a result of the Compact."
But Paul Basari, Compact development officer at the NCVO's Compact Secretariat, said that both sides need to start using the Compact, drawn up to regulate relations between government and the voluntary sector, before any judgements can be passed on its real effectiveness.
"Of course the Compact isn't going to work if people just leave it sitting on the shelf looking pretty," he said. "There's a mediation scheme in existence that should be used when disputes arise, but no-one has taken it up yet. It's pretty pathetic to start criticising something you're not using properly."
Basari said that upcoming amendments, such as a rewrite of the Compact's guidelines on funding, will go some way to improving its use. The new funding guidelines have been rewritten to include issues such as government partnerships and contracts, as well as grants, in an attempt to reflect the increasing role of the voluntary sector in public service delivery.
"The guidelines for funding should underpin the sector's engagement with government at every level," he said. "The inclusion of local issues in the new guidelines should help define the sector's independence and participation in service delivery."
The report aims to highlight some of the issues encountered by voluntary groups working with the Government through the Compact.
Other areas of concern include a lack of understanding of Compact guidelines by non-departmental public bodies, complicated and time consuming auditing processes and a lack of consistent policies on funding overhead costs.
The new funding guidelines will be launched during Compact Week on 3-9 November. The event is being organised to raise awareness of the Compact across the voluntary sector.