The two Libyan men appeared in court in Valetta, Malta, on Saturday, on charges including hijacking after an airliner on an internal flight in Libya was diverted.
The Airbus A320 was diverted to Malta, 500 km (300 miles) north of the Libyan coast, on Friday (December 23) after the crew reported a man had told them he had a hand grenade.
The men, both believed to be in their mid-20s, were taken to the courthouse in the Maltese capital Valletta under a heavy police presence and dressed in flak jackets.
According to local media reports the two, identified as Moussa Shaha and Ali Ahmed, face several charges including hijacking, holding people against their will and the possession of imitation weapons.
During Sunday's hearing, the two pleaded "not guilty" to the charges including hijacking, local media reports said.