It also insisted there should be a formal role for the devolved administrations in trade negotiations that touch upon devolved policy areas.
The Scottish Government wants there to be “a statutory requirement that the agreement and participation of the Scottish Government and Scottish Parliament should be required where new UK trade agreements would have devolved content, or touch on devolved issues”, it said.
The paper, launched by Constitutional Relations Secretary Mike Russell, also argued the UK Parliament should have to consent to future agreements “to ensure that the interests of all nations of the UK are reflected in any trade agreements”.
Current arrangements for developing trade policy across the UK “are already out of date and not fit for purpose in a situation where the UK is a member of the EU”, the report said.
With Brexit now looming, it called for an “urgent and substantial overhaul” of existing processes and procedures.
Key for Holyrood ministers in this is ensuring Scottish interests are protected - with the paper pointing out the greater importance of the export of fish, seafoods and spirits to the economy north of the border.
The report demanded: “The Scottish Government and Scottish Parliament must have a guaranteed role in all stages of the formulation, negotiation, agreement and implementation of all future trade deals to help industries, protect devolved public services and ensure the highest standards of social, environmental and consumer protection in Scotland and across the UK.”
While SNP ministers have repeatedly argued that both Scotland and the UK as a whole should remain in the single market and customs union after the Britain quits the European Union, they have to “make the necessary preparations for all exit possibilities, in order to support and protect the Scottish economy and our key sectors as much as possible”.
Being part of the customs union gives Scotland tariff-free trade with the EU and also means the country benefits from around 40 trade agreements the EU has signed with third countries.
After Brexit the UK will have to negotiate new trade deals with overseas nations, instead of this being carried out by the EU, as has happened for over 40 years.
“The broad and increasing scope of modern trade agreements means that they often deal with, and merge, a range of reserved and devolved policy areas,” the Scottish Government report said.
“The conduct and content of future trade policy, negotiations and agreements will therefore have very important implications for Scotland, and it is vital that the Scottish Government is fully involved in the process for determining them.”
It also warned it would be “challenging” for the UK to make up for a decline in trade with Europe by selling more to other countries.
The report said: “It is clear that any benefits accruing from the ability to pursue new trade deals would be far outweighed by being outside of the single market and customs union.”
Mr Russell said: “The Scottish Government has consistently argued that the best future for Scotland and the UK is to remain in the EU, or at the least in the single market and customs union.
“But we must do everything we can to protect Scotland’s interests in future trade deals in all possible Brexit outcomes.
“The discussion paper makes a strong case for the Scottish Government and Scottish Parliament having a guaranteed role in the development of trade arrangements and ensuring that the views of the Scottish Parliament are respected.
“This would bring clear benefits for Scottish producers, exporters and consumers - not least protecting Scotland’s NHS from being opened up to private competition, or opening up our markets to chlorinated chicken or hormone-injected beef.”
A spokesman for the Department for International Trade (DIT) said: “The people of Scotland, and the whole UK, will have far more involvement in our future UK trade agreements than current EU agreements.
“Indeed, the Trade Policy Minister is visiting Scotland next week to host a consultation event with the Scottish Council for Development and Industry on future free trade agreements.
“We are committed to working with the devolved administrations on an approach to trade negotiations that delivers the best for the UK as a whole.
“I welcome the opportunity to positively engage with businesses, communities and civil society across the entire country as we work together to develop our independent trade policy for the first time in 40 years.”