EgyptAir Flight 181 had 55 passengers on board when it left Borg El-Arab Airport in Alexandria for Cairo Airport this morning.
There was some confusion over the identity of the hijacker.
Al-Arabiya quoted a foreign ministry official in Cairo as saying that the hijacker was 'not a terrorist - he's an idiot... Nile News previously reported that he was an Egyptian national named Ibrahim Samaha, but in a phone interview with privately-owned ON TV in Egypt, Samaha's wife said he was a passenger among the freed hostages with no links to the hijacking.
The pilot of the plane was threatened by a passenger who had an explosive belt, Egypt's Civil Aviation Ministry initially said, but it was later reported that there were no explosives on board.
Pilot Omar El Gamal has reported a threat from a passenger claiming to have an explosive belt.
Some people were seen escaping the Egyptair plane after hours of being held hostage, including one person leaping from the cockpit window and three people leaving via the staircase.
A tweet from the ministry said only that the situation is "over" and that the hijacker had been arrested.
An EgyptAir passenger plane flying from Cairo to Alexandria was hijacked on Tuesday and diverted to Cyprus, where it landed at Larnaca airport on the south coast, Cypriot police and Egyptian civil aviation authority officials said.
Cyprus President Nicos Anastasiades told a news conference the incident "has nothing to do with terrorism". When a reporter asked if it had something to do with a woman, he replied, "Always, there is a woman". It is unclear what relationship she and the man have.
Flight MS181 landed at Larnaca airport at 8.50 am local time (0550GMT), police spokesman Andreas Angelides said, according to the Cyprus Mail website.
The U.S. Embassy in Cyrus says it is looking into whether any U.S. citizens are involved.
Witnesses said the hijacker threw a letter on the apron of the airport in Larnaca, written in Arabic, asking that it be delivered to his ex-wife, who is Cypriot. He said three other foreigners could not be identified.
Negotiations with the hijacker continued and he soon allowed most of the 60 people on board off the Airbus A320.
Larnaca airport has now been closed, with scheduled flights diverted elsewhere.
The explosion was claimed by the Islamic State extremist group and led Russia to ban all direct flights to Egypt, a critical blow to the country's beleaguered tourism sector which has been largely reliant on Russian customers in recent years.