Both men died after being hit by a connecting cable between the vessels on Tuesday, Albanian officials say.
At least 10 people were killed and more than 400 were rescued, after fire broke out on the ferry in stormy seas.
It is unclear how many passengers are still missing. Rescue helicopters have been diverted after another ship sent a distress signal nearby.
A ship carrying several hundred people near the Greek island of Corfu appealed for help late on Tuesday morning, according to Greek media.
The rescue helicopters had flown to a Moldovan-flagged ship, Blue Sky M, which was believed to be carrying migrants just south of the island of Othonoi, north-west of Corfu, reports said.
Unconfirmed reports suggested armed people were on board the vessel bound for Croatia, according to Greek state TV.
Still searching
Italian authorities said they were continuing to search the ferry Norman Atlantic. They have been unable to verify the precise number of people originally on board.
The operator said 478 people had been on the ferry when it left the Greek port of Patras for Ancona in Italy, but Italy's final tally following the rescue comes to only 437, including those who died.Italian Transport Minister Maurizio Lupi said on Monday that a definitive figure could not be given because of errors on the passenger list, no-shows at boarding or people getting off on a stopover at the Greek port city of Igoumenitsa.
Snapped cable
An Albanian port authority official in Vlore told Reuters news agency that the two seamen had been hit by the broken cable.
"One man died on the spot when one cable broke after it got stuck in the propeller," the official said. "The other died on board a few minutes ago when being assisted by a helicopter medical team."
The BBC's James Reynolds in the Italian port of Brindisi says that Tuesday's tugboat accident underlines the many difficulties faced in this recovery operation.
Monday's rescue operation was conducted amid considerable danger and panic.
As passengers tried to escape from the flames by going on to the deck, they were confronted with freezing cold rain and huge waves while heat from the fire below scalded their feet.
Survivors described scenes of people fighting to get to lifeboat slots and into helicopter baskets. Those rescued have complained that the crew seemed overwhelmed by events.
Some witnesses said that there had been no fire alarms or knocks at the door from the crew to rouse sleeping passengers.
