Constitution Secretary Michael Russell said contingency measures had been put in place to ensure Scots get the medical supplies they need and that support for businesses remains in place.
The Brexit transition period will expire at the end of the year, meaning EU rules and regulations no longer apply in the UK.
No deal on future trade and other arrangements have yet been reached with the EU.
This has prompted concerns of widespread disruption, particularly on the Channel crossings through which lorries bring vital commodities into the country, such as food and medicines.
“It is beyond belief that, in the midst of a global pandemic, Scotland is just five weeks away from being removed from the EU single market and customs union against its will by the UK Government," Mr Russell said.
“Whatever the outcome of the current negotiations between the UK and the EU, we know Scotland’s economy and its communities are facing unnecessary damage at the worst possible time.
“The Scottish Government will continue to do everything we can to mitigate against the consequences of the UK Government’s reckless actions to support, as much as we can, our economy, health services and vulnerable communities."
As talks between the UK and EU continue, a no-deal scenario remains a possibility.
But even if an agreement is struck, it would mean the UK leaving the single market and the customs union, as well as an end to freedom of movement.
Mr Russell said the Scottish Government’s resilience room (SGORR) will activate in December to co-ordinate the Government response to the "most significant issues" arising post-Brexit.
Ministers will also work with other UK administrations to ensure patients get the medicines and medical supplies needed.
The Banking and Economy Forum will also be used to help firms struggling with cash flow, while Scottish Enterprise will offer targeted advice and guidance to 1,200 companies assessed as being "particularly vulnerable”.
A £30 million fund is also being made available to enable local authorities to tackle financial insecurity over the winter, while government agencies will also work with universities and colleges to ensure graduates are being prepared for a post-Brexit labour market.
Almost two-thirds of Scots voted to remain in the EU in the 2016 referendum, but the weight of votes south of the Border swung the outcome in favour of Leave. The Scottish Government has stepped up calls for another independence referendum in the aftermath of EU departure.
Mr Russell said: “We will continue that work throughout the transition period and beyond, but the stark truth is that we simply cannot avert every negative outcome and our view is clear that the best future for Scotland is to become an independent country.
“Only by becoming independent can Scotland look forward to once again becoming an equal partner in the EU and take advantage of all the benefits that membership brings.”