The union says that the £26.4m in the scheme could disappear into the budgets of individual councils
London Councils, which represents local authorities in the capital, has run the scheme for London-wide voluntary sector projects since 1986.
But a consultation on its future ended yesterday and some council leaders are keen to see funding for the scheme returned to individual councils.
Doug Nicholls, Unite national officer for the not-for-profit sector, said: "A worst-case proposal could see funding for 400 projects end on 31 March next year and future funds disappearing into the overall councils' budgets with no ring-fencing or guarantee that it would go to the voluntary sector to support the most disadvantaged."
Unite has called for the retention of a London-wide funding scheme for services provided by voluntary organisations and has written to Boris Johnson, the Mayor of London, and Ken Livingstone, the Labour candidate for the 2012 mayoral election, seeking their responses to this proposal.
A decision on the future of the grants scheme is expected this month.