Samso Rederi will still carry those suspected of having coronavirus, as long as they stay in their cars.
The Danish ferry company said in a Facebook post that following the transfer of the first passengers who were quarantined as a result of Covid-19, it has introduced a new procedure.
Passengers have to notify the company if a case of the virus is suspected before they travel.
"We will make sure that you get safely across the water, while at the same time the other travellers should not be worried about any contagion risk," the company said.
"You are going to sit comfortably in your car on the ferry's car deck during the crossing."
Those with suspected cases who are not travelling by vehicle will not be allowed on board or in waiting rooms.
The company's two ferries provide the only way of getting to the island of Samso from other parts of the country.
On Wednesday, another Baltic operator, cruise ferry player Viking Line, warned investors that it had torn up the profit guidance it gave last week as the coronavirus hits its business.
"As a result of the coronavirus (Covid-19), operating conditions in our markets have deteriorated significantly," the company said in a profit warning on Wednesday.
"It is still too soon to quantify the impact on results since there is great uncertainty regarding developments. Therefore, our earlier business performance outlook no longer applies."
