Current recipients had to re-apply for the scheme, which will be phased out by 2014
The charities Community Service Volunteers, BTCV and the Community Development Exchange have confirmed that their applications for a further round of funding under the government's strategic partners programme has been turned down.
The online youth charity YouthNet said that its funding under the programme has come to a "natural conclusion", but declined to say whether it had applied for funding for 2011/12.
The strategic partners programme provided £12.2m in 2010/11 to fund 42 voluntary sector organisations to advise the Office for Civil Society, but the programme is due to be phased out by 2014.
Existing partner organisations were told by the OCS that they would have to reapply for funding of no more than £500,000 per year until the programme ends. Several charities have now been told that their applications were ruled out at the first stage.
The volunteering charity CSV, which received £1.1m from the programme in 2010/11, issued a statement saying it was "deeply disappointed" about the OCS decision. A spokesman said he was unable to comment further.
BTCV, which arranges volunteering placements on conservation projects and received £331,200 from the programme in 2010/11, said in a statement: "BTCV is disappointed to lose its Office for Civil Society funding. In the coming months, despite the loss of our grant, BTCV will maintain its role as a forward-looking civil society organisation."
A spokeswoman for the charity added: "There will be no further statement or interview on this."
A Community Development Exchange spokeswoman said the charity's application had been ruled out at the first stage.It received £252,602 from the scheme in 2010/11, which represented 87 per cent of its income.
"We are incredibly disappointed," she said. "We will be able to carry on until December using our reserves, and are hoping to win some contracts for project work. We have made one of our six staff redundant and our three full-time staff have had their hours reduced. We will have to cut down on the practical support we provide to community development workers."
The youth volunteering charity YouthNet, which received £484,600 from the programme in 2010/11, issued a statement in response to a question over whether it had got through the first round.
It said: "We are currently working with the OCS as our relationship with them changes with the natural conclusion of our strategic funding."
Asked whether the funding had concluded, a spokeswoman for the charity said yes, but added that she was not able to answer any further questions about whether this meant the charity had applied for transition funding and had its application ruled out at the first stage. "I know that is what readers will infer from our statement, but that is all I am allowed to say at present," she said.
Volunteering England is one of the charities whose applications for the transition funding will be considered at a second stage by the Office for Civil Society.
The charity will be interviewed by the department about its bid for £500,000 from the programme. It received £1.6m from the scheme in 2010/11, the highest of any of the strategic partners.