The Scottish Licensed Trade Association (SLTA) market review surveyed 500 outlets across Scotland and found 17% report issues caused by Brexit such as less bookings or loss of staff.
One in four expect to lose staff due to the UK leaving the EU, with 65% expecting wider staffing issues to continue.
Other results show a more positive picture for the industry, with a rise in outlets showing growth from 39% at the end of 2017 to 48% a year later.
But one in seven are in serious decline, rising to 21% in rural areas.
Despite the concerns, there is increased optimism among retailers.
At the end of 2018 around one in six (59%) were either growing or stable and this is projected to rise to 66% by the end of 2019.
SLTA managing director Colin Wilkinson said the survey indicates the key challenges in the sector.
“After a number of years of decline, our summer report indicated a recovering market and this trend has continued over the festive period, with 69% of outlets either growing or stable at Christmas versus 59% for the whole of 2018,” he said.
“However, there are concerns, particularly around Brexit and in rural outlets, where pubs are critical to the community, and key employers.
“Within rural/countryside pubs over 20% are in serious decline.
“Our members are also concerned about Brexit, with 40% anticipating losing staff with whom they have invested in training and 17% already seeing negative impacts.
“Looking forward, we anticipate a continued recovery in 2019 with the growth being led by food, online bookings and locally sourced gins and beers.”
Alistair McAlinder, of survey sponsors KPMG, said: “Unsurprisingly, Brexit has been cited as a key challenge, with associated staffing-related considerations of most concern.
“Whilst uncertainty persists, it remains unsettling for business owners and employees alike.
“In order to provide necessary practical support to staff and to minimise potential disruption, operators should seek to understand options for employees and the possible cost implications.”