The dozens of hostages freed were in a ship hijacked south of the Seychelles in March 2012.
Of the 29 crew members seized, one died during the hijacking and two died from illness while in captivity, according to the organization, Oceans Beyond Piracy.
The hostages were all men from Cambodia, China, Indonesia, the Philippines, Taiwan and Vietnam, it said. They were aboard the Omani-flagged fishing vessel Naham 3 when they were captured.
John Steed of Oceans Beyond Piracy said the crew of Naham 3 was released Saturday. He did not provide specifics on the terms or conditions of their release, or whether any ransom was paid.
They will be repatriated using a UN flight and sent to their home countries, he said in a statement.
"They are reported to be in reasonable condition considering their ordeal," Steed said. "They are all malnourished. Four are currently receiving medical treatment."
Second longest- held hostages
The Naham 3 crew members are the second longest- held hostages by Somali pirates, Steed said.
The longest-held hostages are four crew members of the FV Prantalay 12 vessel who were released
two months shy of five years in captivity. Somali pirates seized them
at sea in April 2010 and released them in February 2015.
Somali pirates and their peers have made millions in ransom money hijacking vessels in the region.
Although piracy off the coast of Somalia has plummeted in recent years, it was an international nightmare at its height, hurting economies and sending the cost of living soaring.
At the time, it cost the global economy $18 billion a year in increased trade expenses, according to a UN study released in 2013. It decreased maritime activity in affected waters and drastically reduced tourism in surrounding nations.