Holidaymakers and business travellers may face increased costs if an exit vote leads to a fall in the value of sterling, according to a report by travel organisation Abta.
Travel businesses may also raise prices in order to recoup the cost of new taxes and levies being introduced, the research found.
Abta said that another potential factor which could make travel more expensive is consumers needing to cover additional health insurance costs if the UK leaves the European Health Insurance Card scheme.
The report, which was produced with economic analysis by Deloitte, also claimed that staffing costs could rise following a vote to leave in June's referendum because travel firms currently enjoy "easy and cost effective" recruitment of EU migrants due to the free movement of people.
The research concluded: "In the longer term, following a Brexit, travel is likely to become more expensive."
Abta chief executive Mark Tanzer said: "Our assessment of the report's findings is that a vote to leave will lead to uncertainties and may lead to increased costs for travel businesses and the travelling public.
"We recognise that people will approach this referendum by considering many factors - personal, professional and economic - before casting their vote.
"Abta has considered what a vote to leave the EU might mean purely from a travel perspective. Our view is that the potential risks and downsides are not matched by an equal upside for the traveller."
Andrew Swaffield, chief executive of low-cost airline Monarch, claimed that the UK leaving the EU could lead to an increase in air fares and a reduction in the number of flights.
He said: "If the UK were to exit the EU, Monarch would view the outcomes for the travel sector as very negative, not least because of the uncertainty that would follow in the aftermath.
"This sweating period after the exit would be very damaging for the sector. An exit would most likely lead to higher air fares and fewer scheduled flights between the EU and the UK.
"It could also bring an end to the European Health Insurance Card and shared tax laws that benefit many British home owners and expatriates living in the EU."
Doreen McKenzie, owner of Belfast-based travel agent, Knock Travel, claimed a vote to leave would be "disastrous" for the travel industry.