The organisation made the comments in response to a Renewable Heat Incentive (RHI) consultation, which ends today, 27 April.
Proposed changes include issues with tariff rates, the introduction of a budget cap and removing support for solar thermal panels from the scheme.
It is also estimated Scotland's growing biomass industry could be affected by the changes.
Both the Committee on Climate Change and Secretary of State for Energy, Amber Rudd, acknowledged last year that the UK is currently on course to miss its 2020 target of meeting 12% of heat needs through law-carbon sources.
However, Stephanie Clark, Policy Manager for Scottish Renewables, said that while the organisation supports the consultations aims to help build sustainable markets and support renewable heat technologies for the right uses, a number of proposals will "significantly impact the industry".
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"The biomass industry in the UK has taken a number of years to develop and in the process has created thousands of jobs in development and supply chain businesses across the country," she said.
"Scotland has been perfectly-placed to capitalise on this because of its geography, high heat demand and plentiful supplies of timber.
"Changes proposed in the RHI consultation will limit opportunities across the board. They will also disproportionately impact the public sector, which has been the driving force behind a number of renewable heat projects in Scotland."
Plans to remove solar thermal panel support have also been criticised, as the technology has been widely adopted by housing associations and was rated top for reliability and ease of use by householders in a DECC survey in January 2016.
Ms Clark added: "The particular strengths of solar thermal panels – which are now at risk of having their support removed – include negligible running costs, and that they can be added to existing heating systems.
"They also work effectively in built-up urban areas and on smaller roofs, broadening the opportunities for homes to invest in renewables."
"As things stand, both the UK and Scottish Governments are likely to miss their renewable energy targets."
(LM/MH)
