The company, which has a travel agency division including Stewart Travel, as well as a long-awaited resort project in Crete, made the prediction as it announced its half-year results to investors.
Minoan’s chairman Christopher Egleton said the referendum vote to leave the EU would have “significant impacts on both our businesses”.
“In travel, it is likely to put up the cost of travel and holidays, which may affect the level of bookings going forward although increased prices may also result in higher commission,” said Egleton.
Minoan’s travel division saw its gross profits rise by 19% to £3.5 million for the six months to April 30 as the total value of transactions rose by 15% year-on-year to £33.1 million for the half-year.
But the company’s overall operating loss widened slightly from £302,000 last year to £310,000 in 2016, while higher finance costs pushed its pre-tax loss up from £759,000 to £1.056 million.
In March, Minoan Group admitted it was exploring the possibility of breaking up the business in order to accelerate growth in its travel agency division.
Egleton added: “Discussions regarding the plans for our travel business are in progress with advisors and others. I expect to be able to give shareholders more information in the near future.
“Our travel business has continued to expand organically and invest for future expansion.
“While with regard to our Crete project, we are encouraged by the shortest possible delay in the hearing of the appeals against the issuance of the presidential decree granting outline planning consent for the Group’s project in Crete.”
Brexit to increase holiday prices says Minoan boss
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