Defence Minister Rajnath Singh's flight is among at least 11 flights that were diverted from the Delhi airport on Friday evening after heavy rain and thunderstorm in the national capital and surrounding areas, news agency ANI has reported.
Some flights were diverted to Lucknow and Jaipur with flight operations hit in Delhi.
Delhi Airport authorities have advised passengers to get in touch with the airlines for updated flight information.
"Due to bad weather, flight operations at Delhi Airport are affected. Passengers are requested to get in touch with the airline concerned for updated flight information," Delhi Airport posted on its official Twitter handle.
The rain, which started in the afternoon and then picked up pace late evening, provided much-needed respite from the sweltering heat in the national capital.
Many residents took to social media to share pictures and videos as rains battered the dry and dusty roads.
Earlier on Thursday, the maximum temperature rose to 43.6 degrees, three degrees above normal, at Safdarjung, the city's base weather station.
The weather department has predicted thunderstorms with gusty winds on Saturday. Partly cloudy sky and rains are likely to keep the mercury in check for the next three to four days.
A cyclonic circulation persisting over Punjab and Haryana will lead to intermittent thundershowers on Saturday, weather forecasters said.
A fresh western disturbance will lead to rain and thunderstorms in northwest India starting Sunday. As a result, the maximum temperature in Delhi will drop to 37 degrees Celsius by Tuesday.
"Back-to-back western disturbances will continue to give intermittent respite from the heat. No heatwave is likely for a week," said Mahesh Palawat, vice-president (meteorology and climate change) at Skymet, a private weather forecasting agency.