The Chief Executive of Scottish Renewables said such a move could also set back the growth of the green energy technology.
The warning follows reports that David Cameron is considering promising new restrictions on onshore windfarms as part of his offer to voters at the next general election.
It is thought that this could include subsidy cuts.
Scottish Renewables said that would make current and future projects less viable.
Chief executive Niall Stuart said: "Axing onshore wind would be bad news for the economy, the environment and employment across Scotland.
"In Scotland alone the industry supports almost 3,400 jobs, with many more dependent on the sector. More than £1bn was invested in 2013, with much more to come.
"The technology is the cheapest large-scale source of renewable power, is already on track to be cheaper than new nuclear generation and is increasingly competitive with gas."
He also warned that without onshore wind the UK would either miss its 2020 climate change targets or have to source renewable energy from abroad, meaning higher costs.
Reports suggest that Mr Cameron is considering making a pledge on the issue in the Tory manifesto for the 2015 general election.
The Conservatives are understood to be sympathetic to complaints that turbines blight the landscape and the noise can cause significant problems for those who live nearby.