After the EgyptAir plane landed at Larnaca airport, the hijacker released all the people onboard except five foreign passengers and the crew, EgyptAir said.
About 60 people, including seven crew, had been onboard, Egyptian and Cypriot officials said.
"The negotiations with the hijacker have resulted in the release of all the plane passengers with the exception of the crew and five foreigners," the airline said in a statement.
Egypt's Civil Aviation Ministry said the plane's pilot, Omar al-Gammal, had informed authorities that he was threatened by a passenger wearing a suicide explosives belt and forced him to land in Larnaca.
A Cyprus Foreign Ministry official said he could not confirm the man was rigged with explosives. The hijacking occurred in Cyprus's flight information region.
Cyprus broadcasting (CYBC) reported that the hijacker may have personal motives. He had an ex-wife in Cyprus, CYBC said.
"The negotiations with the hijacker have resulted in the release of all the plane passengers with the exception of the crew and five foreigners," the airline said in a statement, but it later changed the figure to four foreigners still held.
The plane was an Airbus 320, Egypt's aviation ministry said.
Eyptian state media named the hijacker as Ibrahim Samaha, an Egyptian, but gave no other details about him.
Passengers on the plane included eight Britons and 10 Americans, three security sources at Alexandria airport said.
Israel scrambled warplanes in its airspace as a precaution in response to the hijacking, according to an Israeli military source.
Egypt's vital tourism industry was already reeling from the crash of a Russian passenger plane in the Sinai in late October.
President Abdel Fattah al-Sisi has said it was brought down by a terrorist attack. Islamic State has said it planted a bomb on board, killing all 224 people on board.
Cyprus has seen little militant activity for decades, despite its proximity to the Middle East.
A botched attempt by Egyptian commandos to storm a hijacked airliner at Larnaca airport led to the disruption of diplomatic relations between Cyprus and Egypt in 1978.
In 1988, a Kuwaiti airliner which had been hijacked from Bangkok to Kuwait in a 16-day seige had a stopover in Larnaca, where two hostages were killed.