It was not clear how many people were on board the boats during Thursday's getaway, although some reports suggested the presence of at least 30 fishermen.
Local residents of Lasqorey, a village where the Egyptians were being held, confirmed seeing the boats leave the coast.
"I think some of the pirates are dead because one of them told me that the crews fought them and managed to get away with the boats," Ali Guled, a pirate in Lasqorey, told the AFP news agency.
Al Jazeera's Mohammed Adow, in the Kenyan capital Nairobi, noted that the fishermen had made a "daring and dramatic escape" by taking matters into their own hands.
"The pirates were celebrating the release of an Italian tugboat which had been taken alongside the two Egyptian fishing boats and for which they had been paid $4m in ransom," he said.
"The five pirates guarding the boats were said to be drunk, and the fishermen took advantage of that and attacked the pirates. They are said to have killed two of them and sailed off to Yemen."
The case highlights how illegal fishing off Somalia's coast is one of the "core issues creating the continuation of piracy", our correspondent said.
"The Somali pirates are saying they are just doing what they are doing to guard their country's resouces, and particularly the country's marine resources, which they say all kinds of people from different nationalities are coming in to take advantage of their country's lack of central authority."
In a related development, amid concern about a possible rise in attacks as the monsoon winds ease, officials from the region met military officials from Nato's anti-piracy force on Thursday.
"We had talks with the Nato military officials on board one of their ships ... in order to prevent the pirates from carrying out attacks after the monsoon winds end," Muse Gele Yusuf, a Puntland governor, said.