Both men died after being hit by a connecting cable between the vessels on December 30, Albanian officials say.
At least 11 others 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.
Italian authorities said they were continuing to search the ferry Norman Atlantic. An 11th body was found on December 30.
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.
Prosecutor Giuseppe Volpe told reporters in the Italian port of Bari that it was likely that other victims would be found on the wrecked ship because a number of those rescued had not been on the passenger list.
Italian Transport Minister Maurizio Lupi said on December 29 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.
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.”
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