The economic research institute questioned 320 businesses following the vote on leaving the EU.
The survey found more than 60% of Scottish firms believe Brexit would have a "negative impact" on them.
However, the institute said there was little evidence of companies cancelling investment or recruitment outright.
The Fraser of Allander Institute, an independent research body based at the University of Strathclyde, carried out the survey between 5 July and 12 July, in the aftermath of the EU referendum.
Just over 60% of Scottish firms surveyed said they believed Brexit will have a negative impact on their business, while only 19% said it would have a positive impact. One third said the impact would be "very negative".
About 40% believe that leaving the EU could lead to a decrease in their investment and expansion plans, and 34% said that they could cut back on recruitment.
More than 70% of firms surveyed as part of the research had done no preparation for the UK exiting the EU.
Two-thirds of businesses said resolution of the uncertainty in the economy was a key issue in the negotiation of the UK's exit from the European Union, while 49% of firms cited access to the single market as a key issue.
However, the survey found little evidence of companies actually cancelling investment or recruitment plans.
A quarter of firms said they had made a decision to change their investment and recruitment plans, though the vast majority - 95% - said that decisions had been postponed rather than cancelled entirely.
Prof Graeme Roy, director of the institute, said: "This is the first hard survey evidence post-referendum of what businesses in Scotland are thinking and how they are responding to the unexpected EU referendum result.
"A clear majority believe that the impact - certainly in the short to medium term - will be negative. The survey offers some evidence that investment and recruitment plans may be being put on hold.
"Resolving the current political and economic uncertainty must now be the key priority. The longer the period of uncertainty continues, the more damaging the impact will be on the economy."

The 61-38 vote on the Convention on the Rights of Persons with Disabilities meant the treaty failed to reach the two-thirds majority needed.
Disabled former senator and Republican presidential candidate Bob Dole, who uses a wheelchair, appeared on the floor of the Senate in support.
The treaty was signed by 155 nations and ratified by 126, including Britain, France, Germany, China and Russia.
It says all nations should work to ensure that disabled people enjoy the same rights and freedoms as other citizens.
The treaty was backed by Mr Dole, who was disabled in World War II, Arizona Senator John McCain, who sustained disabling injuries in the Vietnam War, Indiana Senator Richard Lugar, the top Republican on the Foreign Relations Committee, and former Attorney General Dick Thornburgh.
However, only eight Republican senators voted in favour of the treaty.
Others, like Oklahoma Senator Jim Inhofe, said they voted against the measure because of the extra regulation it would bring with it.
"I do not support the cumbersome regulations and potentially overzealous international organisations with anti-American biases that infringe upon American society," Mr Inhofe said.
The White House said it was "disappointed" that the "overwhelming majority" of Senate Republicans voted against the treaty.
Ratification of the treaty "would position the United States to support extending across the globe the rights that Americans already enjoy at home. This in turn would improve the lives of Americans with disabilities" who choose to live or travel abroad, the White House added.
Massachusetts Democratic Senator John Kerry, who backed the treaty, said: "It really isn't controversial.
"What this treaty says is very simple. It just says that you can't discriminate against the disabled."
Supporters also said ratification of the treaty would not require any changes to US law.
The 1990 Americans with Disabilities Act, which sought to protect equal rights for the disabled, became the basis of the UN treaty.
It was negotiated under former President George W Bush's administration and signed by President Barack Obama in 2009.
About 10% of the world's population - or 650 million people - are disabled, UN estimates suggest.
Most Scottish firms believe Brexit is bad for their prospects and the economy, according to a survey by the Fraser of Allander Institute.
[NEXT_CONCEPT]
A UN treaty on disability rights has been rejected by the US Senate.