The men remained missing late Sunday night. They had been scheduled to appear before a magistrate Monday about their first escape — from the same prison — three years ago.
The shaken government quickly dismissed three Justice Ministry officials, and the prime minister scheduled an emergency meeting of part of his cabinet Monday to discuss the country's prisons.
"This was an insult which I will not accept ... I will take measures as harsh as necessary," Justice Minister Nikos Dendias announced.
Vassilis Paleokostas, 42, and Alket Rizaj, 34, were picked up by a helicopter that flew over the courtyard of Athens' Korydallos prison Sunday afternoon. They climbed a rope ladder thrown to them by a woman passenger, the Justice Ministry said.
Guards on the ground opened fire and the woman fired back with an automatic rifle, authorities said. No injuries were reported.
Police said an elderly couple found the helicopter abandoned near a highway north of Athens, with its fuel tank leaking from a bullet hole.
The pilot was bound and gagged, with a hood over his head. He told police the helicopter was chartered by a couple who said they wanted to go from the town of Itea in central Greece to Athens. The couple had chartered the helicopter a number of times in the previous weeks.
This time, the pilot said, the couple threatened him with an AK-47 rifle and a grenade and forced him to fly to the prison.
Despite their previous escape, the two inmates had been allowed to take their daily walk on the prison grounds together on breaks from solitary confinement.
Their first escape by helicopter was on June 4, 2006. That operation had been masterminded by Paleokostas' elder brother Nikos, himself a convicted criminal who escaped from the same prison in 1990 during a mass breakout.
The elder Paleokostas was recaptured and is still in jail. He has been convicted of 16 bank robberies.
Rizaj, an Albanian immigrant, was also recaptured in September 2006, while Vassilis Paleokostas was captured in August 2008.
While on the run, Paleokostas is suspected of masterminding the June 2008 kidnapping of a prominent Greek industrialist, Giorgos Mylonas, who was held for 13 days until his family paid a ransom.
Police are investigating whether Rizaj was involved in contract killings during the three months after his previous escape.
Dendias, the justice minister, announced that he had asked for and obtained the resignations of the general secretary of the ministry, the inspector-general of prisons and the head of the Korydallos prison.