Seif El Din Mustafa is charged with hijacking, kidnapping, threatening violence, threatening use of explosives and civil aviation law violations, according to Cyprus police.
He admitted to the crimes in court Wednesday.
"He confessed before the judge in the court, it is a guilty plea," Cyprus police told CNN.
Mustafa remains in custody and faces further interrogations, police said. Investigators are also taking additional statements from passengers.
Mustafa is accused of hijacking EgyptAir Flight 181 en route from Alexandria, Egypt, to Cairo on Tuesday. He held the passengers and crew hostage with a fake explosive belt.
The incident ended relatively peacefully Tuesday when the plane's crew and passengers left the aircraft and authorities took the hijacker into custody.
Mustafa allegedly hijacked the EgyptAir flight because of his ex-wife, officials said. The hijacking was not related to terrorism, a spokesman for the Cyprus Transport Ministry said.
The hijacker was "unstable," Homer Mavrommatis, director of the Cyprus Ministry of Foreign Affairs Crisis Management Center, told CNN. Egyptian authorities negotiated with him, but Mavrommatis said his motivation was not clear.
"He kept on changing his mind and asking for different things," Mavrommatis said.
This is not Mustafa's first brush with the law, Egypt's Interior Ministry said. The 58-year-old has a criminal record that includes "forgery, impersonation, burglary and drug dealing," the ministry said.
Mustafa was sentenced to one year in prison for forgery and escaped in 2011, officials said. After additional legal procedures, his sentence for forgery resumed on January 5, 2014, and he was released almost exactly one year later.
The Airbus 320 was carrying 70 people: 55 passengers, including the hijacker, seven crew members and, because it was a connecting flight, an additional eight crew members, according to EgyptAir's Dina El Foly. Officials said earlier that as many as 82 people were on the plane.
Many of the passengers and crew were released during the early stages of the ordeal, Egypt's Civil Aviation Ministry said.