In a letter to Holyrood's Rural Economy and Connectivity committee, the SNP Minister revealed that 166 businesses have been overpaid through the government’s cash advance loan scheme.
Human error has been blamed for a mistake in the formula for converting Euros into Sterling, which affected a quarter of those receiving money in the November 24 payment run.
Mr Ewing said the farmers who were overpaid will be given 30 days to pay back the money, which amounts to £746,000. However, in a separate letter to the Public Audit Committee on the same issue, the Permanent Secretary provided no such time frame.
The national loan scheme was established after a catalogue of problems with farm subsidy payments and the collapse of a £178million IT system for processing applications.
Scottish Conservative MSP Peter Chapman, Shadow Secretary for Rural Economy and Connectivity, said: “This is yet another blunder by a government which has an abysmal track record on the distribution of vital farm payments.
“Whilst a relatively small number of businesses have been affected, this incident simply further erodes confidence among the farming community.
“NFU Scotland has already pointed out that any goodwill that has been built up from the establishment of the loan scheme has now been undermined.
“There have been precious few signs so far that there won’t be further issues with next year’s farm payments."
Jamie Greene, MSP for West Scotland and who sits on the Rural Economy Committee, added: “The Scottish Government’s handling of rural affairs is increasingly worrying. We’re now approaching a full year of disruption for Scottish farmers.
“It’s astounding that the Scottish Government has wasted nearly £1million of taxpayers’ money because it couldn’t handle something as basic as working out the correct exchange rate.
“This should raise some serious questions about this government’s ability to manage our rural economy.”