An even larger number, 41% of respondents, said it has had a negative impact on new investment with only 3% stating it had been positive.
Another third said it has had a negative impact on staff recruitment with again only 3% feeling bullish.
Overall, around half of the businesses surveyed said that the decision so far has had no impact on their business activity. Only 6% said it had been positive, with 44% saying the impact had been negative.
Despite the hopes that Brexit would open up new export markets to UK firms only 18% of Scottish businesses thought it would lead to opportunities in new markets outside of the EU.
Just over half, 51%, of businesses said they did not see any immediate benefits from Brexit, however 28% said there might be benefits from moving away from EU regulations. Over a quarter pointed to the possibility of increased funding from the Scottish or UK Government in the future.
Scottish firms said there is not enough information currently available to enable them to plan for potential Brexit outcomes with 59% bemoaning ?uncertainty over the UK Government’s objectives in the negotiations?.
The Institute also spoke to businesses about their experience in engaging with government and public agencies to help them prepare for Brexit. Only 5% said that they had “sought guidance from government to assist with Brexit planning”.
Fraser of Allander said in a blog alongside the survey that it was “hard to believe from an economics perspective that ?we are in a position where senior UK ministers are openly talking about not just a hard Brexit, but no deal?.
It added: “The overwhelming view amongst the majority of economists is that such a dislocation of trade patterns with our largest trading partner will have significant negative implications for jobs, investment and prosperity.
“Brexit is happening like-it-or-not. So, it is vital that businesses prepare for such an eventuality.
