Defra's Rural Social and Community funding programme for rural voluntary and community organisations is complex and the timescale could prevent some from applying, according to the NCVO.
Defra's consultation on the funding stream began in July and finished in October. The results were not published until the beginning of November, but applicants had only until today to submit their business plans in support of their applications.
The programme, worth £13.5m over two years, is designed to help rural communities, from assisting socially excluded individuals to developing the capacity of the voluntary and community sector.
Claire Steel, rural policy officer at the NCVO, said: "We are concerned that smaller organisations that haven't picked up on this before will not be able to get their work funded through this programme."
Prospective applicants have been encouraged ever since the consultation was launched to form partnerships with a view to applying to the fund.
The NCVO is calling on Defra to allow some flexibility and to encourage partnerships that actively seek to engage smaller organisations.