Krishna, who was in Brazil on an official visit, had cut short his trip and was returning to New Delhi following the death of Andhra Pradesh Chief Minister Y S Rajasekhara Reddy in a chopper crash.
"The pilot of the Emirates flight sought permission from Pakistani authorities to land in Karachi after bad weather developed over New Delhi. The aircraft was granted permission and landed in Karachi at 10.35 p.m.," a television channel quoted Civil Aviation Authority spokesman George Pervez, as saying.
After waiting in vain for over an hour for weather to clear over India, the pilot decided to fly to Dubai at 11.44 p.m. after the aircraft was refuelled, Pervez said.
Reports said that besides Krishna, several senior Indian officials were also on the flight. The total number of passengers on the flight could not be immediately ascertained. No passengers were allowed to leave the aircraft while it was on the ground in Karachi.
The flight has reached Indian capital early this morning.