It also said only a third of the operations would resume in the first phase.
The Delhi airport saw its first departure at 4.45 am to Pune while Mumbai airport's first departure was at 6.45 am to Patna, the officials said.
Several other incoming and outgoing flights are scheduled during the day as the Maharashtra government late on Sunday permitted restricted operations in view of the Coronavirus pandemic that has gripped the state in a big way.
In the evening, cabinet minister Nawab Malik said the Maharashtra government has chose to permit 25 flights to land and take off from Mumbai airport from Monday.
Puri on Saturday admitted that several states have expressed reluctance to resume flights from Monday.
Maharashtra government has allowed 25 takeoffs and 25 landings every day from Mumbai airport. An IndiGo spokesperson said 20,000 passengers will travel on Monday onboard the airline's flights.
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La menace du Covid-19 pèse sur la fin du ramadan partout dans le monde, alors qu'en Europe, le déconfinement se poursuit. Devant lui, des agents de sécurité, certains portant des masques, se tenaient devant quelques fidèles.
GMR Hyderabad International Airport Limited (GHIAL), which is operating RGIA, has taken a slew of measures with focus on a contact-less boarding experience for passengers.
As per the guidelines, all passengers had to register their details with the Covid-19 Jagratha web portal.
Arrival and departure of as many as 80 flights were cancelled at Delhi's Indira Gandhi International airport on Monday, the first day of phased resumption of domestic flights after a two-month suspension, officials said.
"With Andhra Pradesh set to resume operations from tomorrow & West Bengal from 28 May, these numbers are all set to increase further".
Though there was some confusion regarding various states seeking quarantining of passengers after flights, the issue was settled following negotiations between them and the Centre on Sunday.
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Another 20% were "somewhat" interested and the largest group wanted flexibility, with some remote and some in-office work. At the present pandemic condition all the possible companies are shifted to Work from Home strategy for safety purposes.
This led to a cascade of calls at the customer care centres of online travel agents.
Individual states will be responsible for arrival procedures, including 11 which have made quarantine mandatory, including in some cases for two weeks.
The Centre's decision to resume services came as the aviation sector reeled under severe stress triggered by the lockdown in force since March 25. But the prospect of quarantine for 14 days and with no idea what the place will be like, is too much for me to handle. "If your status on the app is green, why should anyone want any quarantine?"
Persons coming from Red Zone areas in Kerala or any zone from other states will be quarantined in Kochi for seven days.
Staff attending to passengers with special needs have been mandated to wear protective gear. In response to a question, he said that they might start global flight services before August-September.
The central government is aiming to restart global flights by mid-June or July, Union Civil Aviation Minister Hardeep Singh Puri said on Saturday. The state government has been reluctant to allow flight operations in the state over fears that it may worsen the already-rising number of covid-19 transmissions in the state.
India records almost 7,000 Covid-19 cases in 24 hours
A total of 130 new cases were reported in the state on May 24. 654 patients have recovered and the state has reported 42 deaths. For the fourth consecutive day , India reported the highest ever spike of 6,977 COVID-19 cases in 24 hours.
Passenger air services were suspended for both scheduled domestic and worldwide flights since March 25, due to the imposition of the nationwide lockdown in the wake of the Coronavirus outbreak.