"The (technical) failure manifested as a strong noise, from an unknown origin, and it was followed by perturbation of the cabin pressure," a government spokesman told reporters in Skopje.
As it was impossible to restore normal cabin pressure, the pilot decided to land at the nearest airport.
No passager or crew member was hurt in the incident and the prime minister was to return to Skopje with another plane, spokesman Aleksandar Gjorgiev said without elaborating.
Gruevski was returning home from Strasbourg where he held talks with opposition leader Zoran Zaev, brokered by the European Parliament, in a bid to end a deep political crisis in his country.
In 2004, a plane carrying the then Macedonian president Boris Trajkovski crashed in southern Bosnia, killing him and all eight other people on board.
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