Farmers in Devon and Cornwall claim they have been "led up the garden path" over diversification grants.
The NFU in the South West said some have spent thousands of pounds applying for cash for projects - only to be told the scheme has run out of money.
The Rural Enterprise Scheme (RES) was set up to encourage farmers to diversify and develop projects such as farm shops and nurseries.
The government said it is looking at alternative solutions.
Although the scheme in its current form is due to end later this year, applications were still being taken by the Department for Environment and Rural Affairs (Defra).
Some farmers have told the NFU they have spent time and money applying for RES cash, but have now been told the funds have gone.
Defra said the scheme has proved very popular and all the available money appears to have been allocated.