Two of the three Panamanians on board the disabled vessel later died.
Princess Cruises said that although passengers on the cruise ship had spotted the castaways and alerted staff, the captain had not been told.
The one surviving fisherman – Adrian Vasquez, 18 – was later rescued after 28 days at sea.
Adrian Vasquez had reported that – after 16 days adrift – he and his companions saw a cruise ship sailing past, despite desperate attempts to flag it down.
Three birdwatchers on board the cruise ship – the Star Princess – said they had spotted the fishermen waving for help and told ship staff, but had been unable to persuade them to change course.
In a statement, Princess Cruises said a preliminary investigation had found that there appeared to have been a “breakdown in communication” in relaying the passengers’ concern.
It said Captain Edward Perrin and the officer of the watch were not notified.
“Understandably, Captain Perrin is devastated that he is being accused of knowingly turning his back on people in distress,” the statement said.
“Had the captain received this information, he would have had the opportunity to respond.”
Princess Cruises added that it understood its responsibility under the law of the sea to help any vessel in distress, and said its ships had been involved in more than 30 rescues over the past decade.
It said the investigation was continuing.
Adrian Vasquez was eventually rescued 1,000 km (620 miles) off the mainland, near the Galapagos Islands.
He said he survived after his friends died thanks to a sudden rainstorm that replenished his drinking water supplies.
Adrian Vasquez told the Associated Press he still felt anger at the ship he saw sail past two weeks before his rescue.
“I said <<God will not forgive them>>,” he said.
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