Adrian Vasquez told officials he was overjoyed when he saw the huge Star Princess headed toward his disabled vessel after trying to get the ship's attention, the Globe and Mail reported.
But instead of slowing down the Star Princess kept going and by the time the fishing boat was rescued near the Galapagos Islands weeks later one of the men was already dead and another died five days later.
A spokesman for the Miami-based cruise line admitted a breakdown in communications occurred.
"Neither Captain Edward Perrin nor the officer of the watch were notified," Carnival said. "Captain Perrin is devastated that he is being accused of knowingly turning his back on people in distress."
The drifting fishing boat was spotted by two passengers from Portland, Ore., who said they notified the bridge.
"We expected the ship to turn back or stop or something," said Jeff Gilligan.
Carnival, the world's biggest cruise line, has suffered a number of mishaps recently. One of its newest ships, the Costa Concordia, sank off Italy in January killing more than 30 people.
In February, the Costa Allegra was left powerless and drifting in the Indian Ocean after a fire broke out.