"If your life is in jeopardy and you're in the Bahamas and you want to get to the United States, you're going to be allowed to come to the United States, whether you have travel documents or not", he told reporters during a press briefing at the White House.
"Everybody needs totally proper documentation", Trump told reporters.
Rubio and Florida's other USA senator, Rick Scott, have asked President Donald Trump's administration to waive visa requirements altogether for Bahamian storm victims with relatives in the us, but Trump indicated Monday that he wants to keep stringent vetting in place in part because of "people going to the Bahamas that weren't supposed to be there".
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 U.S. immigration officials and the operator of the vessel.
Current US policy allows Bahamian residents travelling to America by air to enter the country without a visa as long as they have a passport and proof that they do not have a criminal record. Mark Morgan, the acting commissioner, said there was simply "confusion" over people fleeing the Bahamas being able to come to the US.
"Look, the Bahamas has some tremendous problems with people going to the Bahamas that weren't supposed to be there", Mr Trump said. All of them were properly documented to enter the country, US Customs and Border Protection (CBP) said.
Rubio toured the worst-hit islands last week with his fellow U.S. 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.
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Officials say more than 100 Bahamians who hoped to evacuate to Florida after Hurricane Dorian but didn't have visas were kicked off a ferry because operators failed to coordinate the mission with authorities. A day earlier, a cruise ship arriving at the Port of West Palm Beach carried almost 1,500 refugees, all of whom were processed. "However, Balearia (the ferry operator) did not do that", Mr Silva told CNN.
Authorities in the Bahamas say the death toll from Hurricane Dorian has now risen to 45, a week after the archipelago was battered by the wild weather.
According to the United Nations, at least 70,000 are in need of food and shelter.
Members of the Gainesville, Florida, fire department were operating in the remains of The Mudd, the Bahamas' largest Haitian immigrant community. Immigration officers at points of entry, he said, had discretion "to issue humanitarian or medical parole on a case-by-case basis".
"I'm relieved that we walked away from these talks", Rice said in an interview on "CBS This Morning" on Tuesday. "All of the evacuees possessed valid travel documents".
The only aid they have received so far is from foreign aid groups and USA firefighters, said Reckley's husband, Dexter Edwards, a heavy equipment operator.
A spokesperson for CBP said the 103 Bahamians who were not allowed to travel did not have any kind of identification. None were required to show visas when they disembarked in Florida. Trump said, "We're talking to a lot of people about that". The severity of the damage the islands incurred from Hurricane Dorian is hard to conceptualize.
Former congressman and 2020 presidential candidate Beto O'Rourke responded to the news that displaced Bahamians had been removed from the ferry by criticizing the Trump administration.