The move came as the government revoked the operating license of the owners of the ferry that sank with the loss of around 300 lives, citing safety violations by the company and crew.
The three part-time crew members hailed as martyrs included an engaged couple Kim Ki-Woong and Jung Hyun Seon who could have escaped the sinking vessel but stayed to help trapped passengers.
The third was Park Ji young, 21, the youngest crew member, who became a public hero after it emerged that she had given her life jacket to a passenger as she sought to guide people to safety.
Being designated martyrs entitles them to burial at a national cemetery, and their families will be eligible for financial compensation, medical assistance and other incentives.
The behaviour of the part-timers stood in stark contrast to the captain and most of the crew who were among the first to abandon ship and have been widely vilified for leaving trapped passengers to die.
The Ministry of Oceans and Fisheries said the license revoked on Monday was for the route taken by the ill-fated, 6,825 tonne Sewol from the western port of Incheon to the southern island of Jeju.
The owners, Chonghaejin Marine Co., are also under pressure to give up the licences to its two other routes to outlying islands.
A ministry statement said the action was taken because the company was deemed to have contributed to the disaster, and in light of the behaviour of the captain and crew.
All 15 surviving crew members, including the captain, have been arrested.
The confirmed death toll from the disaster stood at 275, with 29 still unaccounted for as dangerous conditions suspended recovery operations for a third straight day.
Divers have been unable to access the submerged vessel since Saturday morning, with strong tides and heavy swells pushing conditions beyond the safety limit.
The families of those still missing oppose raising the vessel until every body has been retrieved.
But the search, in near zero visibility, is becoming increasingly dangerous, with some partition walls on the ship warping and at risk of collapse.
"We will put the priority on the safety of divers when they search through dangerous areas," coastguard spokesman Ko Myung-Suk told a daily briefing.
The Sewol was carrying 476 people when it sank after listing sharply to one side and then rolling over.
Of those on board, 325 were children from a high school on an organised trip to the southern resort island of Jeju.
Initial investigations suggest the ferry was carrying up to three times its safe cargo capacity.
The Sewol's regular captain, who was off duty on the day of the accident, has told prosecutors that Chonghaejin Marine Co. "brushed aside" repeated warnings that the 20-year-old ship had stability issues following a renovation in 2012.
Five Chonghaejin officials, including the company's head, have been arrested on various charges including manslaughter, negligence and breaches of safety regulations.
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