During the phone call, Modi praised the injured airline captain for his bravery and wished him a speedy recovery, sources told India Today.
While details of the conversation were not disclosed, the sources said Machchhar told Modi what gave him the courage to act after he was allegedly attacked by his co-pilot.
Modi on Thursday lauded Indian pilot Captain Smit Machchhar for his courage during a dramatic mid-air cockpit attack aboard a flydubai flight, saying his actions helped avert a tragedy similar to the 9/11 attacks.
Speaking at an event, PM Modi said that Machchhar demonstrated "patience, wisdom, and courage" during the incident.
"The incident that occurred yesterday and the way in which India's Captain Smit Machchhar demonstrated patience, wisdom, and courage, and today Israel's Prime Minister said that this Hindustani saved us from a 9/11... This feat of Smit fills every citizen with pride," Modi said.
"Today, I also spoke with his father Bhupendra Bhai, his mother Geeta, and his wife Sonal. Today, the entire world is proud of him. I pray to my fellow citizens that we all pray for Smit's long life and good health, and congratulate brother Smit, who has enhanced India's pride," he added.
The conversation came days after Flydubai flight FZ1073, travelling from Dubai to Tel Aviv, was forced to make an emergency landing in Saudi Arabia following a violent confrontation between the two pilots inside the cockpit.
According to reports, the incident began when the Omani co-pilot allegedly attacked Captain Smit Machchhar, an Indian national and experienced commercial pilot. Machchhar reportedly sustained serious injuries during the confrontation.
The aircraft was carrying 174 passengers, including 27 children, when the incident unfolded.
Passengers and crew members reportedly intervened after the cockpit door was unlocked. Israeli dentist Musaev Shota, who was travelling on the flight, said he helped restrain the alleged attacker before assisting the injured captain and attempting to stop his bleeding.
Despite his injuries, Machchhar reportedly managed to unlock the cockpit door before losing consciousness, allowing passengers and crew members to enter the cockpit and help overpower the alleged attacker.
The aircraft also reportedly underwent a dramatic descent during the confrontation before control was regained and the flight was diverted to Saudi Arabia for an emergency landing.
Investigators are examining the circumstances surrounding the cockpit confrontation, the alleged attacker’s motives and any possible links to external actors. Any connection to Iran, however, remains unconfirmed based on the statements cited above.