The Indian Air Force Plane was sent from New Delhi more than two hours later.
PM Modi flew in a helicopter from Deoghar to Bihar's Jamui to attend an event to celebrate tribal icon Birsa Munda's birth anniversary, which is known as Janjatiya Gaurav Diwas.
He then flew back to Deoghar in the chopper and was supposed to return to Delhi when the snag was discovered.
In a similar situation ahead of the Lok Sabha polls earlier this year, Rahul Gandhi's helicopter remained grounded in Jharkhand's Godda for 45 minutes awaiting clearance from the air traffic control.
The delay prompted Congress to claim it was intentional to disrupt Rahul Gandhi's campaign schedule.
The party later filed a complaint with the Election Commission.