The 160 passengers on board the plane have been evacuated.
A man has been taken into custody over the incident.
It is the firs time in 10 years that there has been an event like this at Prague Airport.
A spokesman for Prague’s air traffic control, Richard Klima, said: “An Enter Air plane flying from Las Palmas, Spain to Warsaw landed in Prague because of the threat of an illegal act.
The evacuated passengers will spend the night in Prague and resume their trip tomorrow after a thorough check of the aircraft.
Mr Chovanec declined to say whether or not an explosive device had been found on the detained man before police had finished their work.
However, he later tweeted: “Does not look like a terrorist attack” and “Situation under control”.
This latest terror scare comes as Europe is on high alert for New Year’s Eve following various deadly attacks in 2016.