The row was ignited by a letter sent earlier this month by Dr Bob McIntosh, chief executive of the Forestry Commission Scotland and director of the Scottish Government's environment and forestry division, urging "key stakeholders" to "disseminate [the letter] across your staff and wider networks" in order to "provide as much information as possible to the people of Scotland".
The letter provided links to pro-independence publications produced by the SNP Government but no balancing materials supporting the Union.
Stuart Goodall, chief executive of Confor, which represents about 1200 private-sector foresters and tree harvesters, told the Sunday Herald that he had refused to disseminate the letter. "This wasn't something I felt comfortable forwarding on. Our role with our members is to give them impartial advice and represent their interests. We have also sought to be neutral on the issue of how we approach the referendum itself.
"Dr McIntosh is a civil servant and we would expect the civil service to be 100% neutral and this didn't seem to be entirely compatible with that."
David Sulman, chief executive of the Stirling-based UK Forest Products Association, which represents 60 UK companies (30 in Scotland) said that the letter was out of character from McIntosh, a well-regarded forester.
"I was somewhat surprised by this letter from an arm of government that should be apolitical. The Forestry Commission's focus should be on looking after forestry in Scotland."
But the most vehement criticism came from William Crawford, chairman of the Royal Scottish Forestry Society, a conservation charity "for those who love the forests, woodlands and trees of Scotland".
Posting on the body's website, the former judge issued "a stern word to Dr Bob McIntosh" for issuing "a blatant piece of pro-independence propaganda paid for by us taxpayers".
"We foresters are well capable of making up our own minds about political matters. We do not need advice about how to vote in the forthcoming referendum, still less do [our employees] require pressure to vote in a particular way from [their bosses]. If, as I imagine has happened, a Minister, of whatever political persuasion, seeks to put pressure on you to 'disseminate' his propaganda, your duty, I respectfully suggest, is to tell him to take a running jump."
Russell Brown, Labour MP for Dumfries and Galloway, said: "The mass use of Scottish Government agencies and civil servants to promote independence at taxpayers' expense is an appalling abuse of power by SNP ministers.
"The public pay their taxes for government agencies to spend their time serving communities not to preach SNP propaganda."
A spokesman for Forestry Commission Scotland said: "It is right and proper that voters are fully informed on the issues associated with the referendum. The Scottish and UK Governments are issuing material to assist voters. There is nothing improper in FCS's actions here."