More than a hundred Bahamian citizens desperate to escape the devastation of Hurricane Dorian were ordered off a ferry to Florida, sparking a dispute between US immigration officials and the operator of the vessel.

Crew members aboard the Balearia in Freeport, Grand Bahama, told 119 evacuees without valid US visas they would have to disembark because US Customs and Border Protection (CBP) warned “in a last-minute call” they would not be admitted to the US on arrival in Fort Lauderdale.

Under CBP rules, passengers lacking visas are legally admissible on humanitarian grounds as long as they also carry a police report confirming they have no criminal record. But those with such documentation were asked to get off the Balearia after the passenger manifest was submitted to the US federal agency on Sunday night, according to some of the crew, because they said the US would not accept them.

CBP fired back on Monday. Mark Morgan, the acting commissioner, said there was simply “confusion” over people fleeing the Bahamas being able to come to the US.

“We will accept anyone on humanitarian reasons that needs to come here,” he said at a White House briefing, adding that those with serious criminal records were automatically disqualified.

Stephen Silvestri, the acting director for CBP at Port Everglades, told a reporter from Miami news station WSVN who was onboard the ferry: “If those folks did stay on the boat and arrived we would have processed them, vetted them and worked within our laws and protocols and done what we had to do to facilitate them.”

“I think it was a business decision by Balearia to remove them. They were not ordered off the boat by any government entity.”

The ship’s owners, Balearia Caribbean, did not immediately respond to requests for comment.

In a statement to WSVN on Monday afternoon, the company said it had “boarded the passengers with the understanding that they could travel to the US without visas, only to later having been advised that in order to travel to Ft Lauderdale they required prior in-person authorization from the immigration authorities in Nassau”.

“We regret and apologize for the hardship and inconvenience experienced by the 119 passengers who are residents from Grand Bahama Island who could not be transported,” the company added.

Most of the passengers had spent hours at the crowded dock in Freeport on Sunday, trying to secure a seat on board the 1,000-capacity vessel.

Renard Oliver, an evacuee from Grand Bahama trying to reach Florida with his two young daughters, told WSVN: “They’re saying they just got a call from CBP and CBP told them that everyone that doesn’t have a US visa and was travelling on a police record has to come off.

“At the last minute like this it’s kind of disappointing. It’s hurting watching my daughters cry.”

On Saturday, 1,500 evacuees from Grand Bahama reached Palm Beach, Florida, aboard the Grand Celebration, a ship operated by Paradise Cruise Line. The difference, according to CBP, was that Paradise had coordinated the voyage with Bahamian government and US officials in Nassau, the capital of the Bahamas.

“CBP relies on the transportation companies … to be engaged in ensuring the safety and wellbeing of any individuals that have been devastated by this tragedy and that requires transparent communication and planning for adequate resources to receive any arrival,” a CBP statement issued on Monday said.

Since the category 5 hurricane tore into north-western islands of the Bahamas eight days ago, with winds gusting above 200mph and a storm surge of more than 20ft, thousands have been evacuated to Nassau or the US.

Military transport planes flying from Abaco and Grand Bahama enhanced efforts begun by dozens of operators of private boats and aircraft in the immediate aftermath of the storm.

Marco Rubio, the US senator for Florida, backed the CBP position in a Monday lunchtime tweet, claiming that it appeared Balearia “didn’t coordinate in advance. And decided to leave instead of waiting a few hours to complete process.”

Rubio toured the worst-hit islands last week with his fellow US senator Rick Scott and Ron DeSantis, the former and current governors of Florida, the trio urging the Trump administration to waive or suspend certain visa requirements for Bahamian nationals to come to the US.

In a series of tweets, Morgan, the acting commissioner of CBP, said no visa documentation requirements had changed. Immigration officers at points of entry, he said, had discretion “to issue humanitarian or medical parole on a case-by-case basis”.