Scottish Forestry will remain as a standalone executive agency and will not be included in proposals for a new single environmental body.
Gillian Martin, Scottish Government Cabinet Secretary for Climate Action and Rural Affairs, confirmed the decision in a written response.
The prospect of Scottish Forestry being included in a larger environmental body had faced industry opposition.
The Scottish Government has been considering putting organisations including SEPA, NatureScot and Zero Waste Scotland together, with Scottish Forestry potentially joining them.
Martin wrote: “Following careful consideration of the options for public service reform, I have decided that Scottish Forestry should continue as a stand-alone Executive Agency.
“We will work with colleagues in the current organisations and Scottish Government to ensure continuity during the transition, while supporting the opportunities to deliver more efficient and effective services and better outcomes.
“We will continue to engage closely with our forestry partners and stakeholders to achieve the social, economic and environmental benefits of forestry.
“Our day to day work continues and our stakeholders are assured that activities such as the processing of grant applications and payments, regulatory decisions and felling permissions are being carried out as normal.”