The NCVO has expressed concern at government plans to hand over responsibility for five rural funding streams in England to Regional Development Agencies.
The Department for Environment, Food and Rural Affairs will cease awarding the grants, which include the Rural Enterprise Scheme, in July.
Defra said the change would "better target the needs of rural people and businesses in each region".
But Claire Steel, rural policy officer for the NCVO, disagreed. "Recent research found that the rural voluntary sector has a patchy relationship with the Regional Development Agencies," she said. "We hope the new programme will be more flexible in what it funds."
The Rural Enterprise Scheme will accept its final applications on 30 June.
Defra has announced an extra £100,000 for voluntary bodies that help farmers deal with stress. The announcement comes in the wake of payment delays to farmers by the Rural Payments Agency. Farming Help, an umbrella organisation of five groups offering help and support to farmers, will distribute the extra funds.