The Mentoring and Befriending Foundation and the National Council for Voluntary Youth Services have been told they will no longer receive funding from the Office for Civil Society under its strategic partnership programme.
The Mentoring and Befriending Foundation, which is an umbrella body that provides training and support for mentoring and befriending charities, received about £1.1m from the programme in 2010/11, representing about half of its funding.
The NCVYS received £242,143 in the same period - about 15 per cent of the £1.5m income that is shown for the organisation on the Charity Commission's website.
The OCS announced the withdrawal of its support for the strategic partners programme, which provided £12.2m in funding for 42 voluntary sector organisations to provide advice to government in 2010/11. The funding will be phased out by 2014.
Steve Matthews, chief executive of the Mentoring and Befriending Foundation, said the charity had applied for £350,000 under the scheme for next year. He said it had already made 15 of its 30 staff redundant and could not rule out further redundancies.
"We will continue to exist on our reserves and will try to find other grant funding," he said. "I don't think at the moment that we will have to close."
Matthews said the funding would have been used to help the charity's members to measure their outcomes so that they could start competing for payment-by-results contracts.
Faiza Chaudary, director of policy at NCVYS, said the charity had applied for £296,000 in a joint bid with the Youth Action Network, which had also been a strategic partner of the OCS.
She said no redundancies would be made as a result of the loss of funding.
"The funding would have been used to ask the Cabinet Office to fund consolidation work among charities," she said. "We will have to think of another way of doing this."
Meanwhile, David Tyler, chief executive of Community Matters, said his charity had put in a joint bid with the charity Action for Communities in Rural England and had been put through to the second round of the application process.
He declined to give the exact value of the organisations' bid but said that it was close to the maximum amount of £500,000.
In 2010/11, Community Matters received £261,603 under the scheme and Acre received £210,125.