Changes to Land and Buildings Transaction Tax (LBTT) rules would offer full or partial relief from the tax on non-residential buildings and land in certain areas within the green freeports.
Relief would be available for a period of up to five years on land or property bought or leased for certain commercial activities.
The green freeports are expected to be operational later this year after being jointly announced by the Scottish and UK governments in January following a rigorous selection process.
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The new tax relief will be one of a package of incentives available in the green freeport tax sites, which are designated, underdeveloped areas located in the wider green freeport boundaries.
The Scottish Government will also fund local authorities choosing to offer non-domestic rates relief for certain properties or property improvements within the tax sites for up to five years. This is alongside UK Government support of up to £52 million in start-up funding, and areas such as employer National Insurance relief and customs easements.
Public Finance Minister Tom Arthur said: "We intend Scotland's green freeports to become internationally competitive clusters of excellence. By offering LBTT relief we are trying to boost that process by encouraging businesses to expand and invest in underdeveloped sites with economic potential.
"Scotland's green freeports aim to make a significant contribution to achieving our net zero ambitions and will drive the creation of high-quality, well-paid jobs with fair work practices at their heart, including the payment of the real Living Wage.
"I encourage all interested parties to respond to the consultation which is running for eight weeks. The Scottish Government will carefully consider all responses before regulations are introduced to the Scottish Parliament."
