Farm minister Richard Lochhead has said he cannot guarantee subsidy payments will be paid on time this year.
Earlier this week farm leaders said the prolonged wet weather would continue to cause problems into the winter and failure to receive subsidy monies in December would be catastrophic for some producers.
Both NFU Scotland and the Scottish Crofting Federation sounded a warning over the availability and cost of winter feed supplies amid reports some producers had brought cattle in to feed them during the summer.
NFU Scotland president Allan Bowie said any delay to payments would cause unnecessary worry during an already stressful year.
While, Scottish Crofting Federation chief executive Patrick Krause said some crofters could be forced to get rid of animals due to a lack of feed.
Responding to the concerns, Mr Lochhead said government was liaising closely with both organisations.
“The wet weather is clearly having an impact on production which will hit farm incomes as well as create difficulties during the winter months,” added Mr Lochhead.
“We will continue to monitor the effect the wet weather is having on the industry, given the potential for there to be issues going through into the winter.
“Funding is already available under CAP to support the viability of farming and crofting businesses, which I hope will increase their ability to deal with difficult external impacts such as this.”
When asked if subsidy payments would be paid on time in December, he said: “We are continuing to work to that timescale but cannot give a guarantee at this stage and will provide an update in due course.”