NFU Scotland issued the warning as an estimated Â£328m in single farm payments is made to around 16,700 producers.
They said a leading bank has contacted them to raise fears that criminals may target farm accounts.
NFU President Nigel Miller said: "This year's payment run brings a more immediate threat that requires producer vigilance."
The single farm payment is an agricultural subsidy paid to farmers in the EU.
Mr Miller warned that bogus callers could pose as banks, the police or other trusted organisations in unsolicited calls to farmers and landowners.
He added: "The reminder is that your bank would never ask you over the phone to transfer money to protect your account from fraud.
"If you receive a call of this nature, or any call you are suspicious of, you should end the conversation and call your bank on a trusted number, using a different phone line if possible.
"The good cheer brought by having SFP safely in the farm account for Christmas would quickly dissipate were anyone to fall for this cruel scam."
Scotland's farmers have been warned that they could be targeted in telephone banking scams.