Khan had taken off for home from New York's JFK International Airport on Friday evening in a special jet placed at his disposal by the Saudi government, but it flew back in a couple of hours to have the problem fixed, Pakistani media reported.
According to reports, the technical fault was being fixed and there was no cause for concern. The fault was noticed when the airplane was near Toronto.
Imran Khan is to spend the night in a private hotel in New York while the flight will be rescheduled after fixing the fault.
A Pakistani delegation, including Foreign Minister Shah Mehmood Qureshi, is accompanying Imran Khan. There was reportedly an issue in the plane's electronics system.
Pakistan's Ambassador to United Nations, Maleeha Lodhi, who had earlier seen off Imran Khan, rushed back to the airport.
Imran Khan, who led the Pakistan delegation to the 74th session of the UN General Assembly, waited at the airport for some time while technic tried to fix the fault, but since more work was needed, they decided to fly on Saturday morning.
Lodhi escorted the Prime Minister back to the Roosevelt Hotel where he was staying during his hectic seven-day trip.
Officials said if the plane is not fixed in the morning, Imran Khan would take a commercial flight back to Pakistan where he is anxious to visit earthquake-hit areas and visit the affected families.
( With inputs from IANS )