Pakistan Foreign Affairs Minister Shah Mahmood Qureshi in a video interview said India had made a request that Prime Minister Modi's aircraft be allowed overflight on September 20 while flying towards Germany on way to the US, and on its return journey on September 28.
"But keeping in mind Kashmir and India's attitude and its human rights violations, we have decided against granting overflight. And the decision has been conveyed to the Indian High Commission," he said.
The Ministry of External Affairs spokesperson Raveesh Kumar in a statement said that India "regrets the decision of Pakistan to deny overflight clearance for the VVIP special flight for a second time in two weeks, which is otherwise granted routinely by any normal country.
"Pakistan should reflect upon its decision to deviate from well established international practice, as well as reconsider its old habit of misrepresenting the reasons for taking unilateral action," he said.
Earlier, this month Pakistan had denied permission to Air India One carrying President Ram Nath Kovind, to fly over its airspace during an official trip to Europe.
India had earlier formally requested Islamabad to give permission for PM Modi's plane to use Pakistani airspace. For all VVIP visits, the foreign countries are required to be informed of the use of their airspace.
According to the ICAO or International Civil Aviation Organization charter, denial of airspace cannot be done by any country, except in the event of war.
PM Modi is to visit the US from September 21 to 27 where he will address the United Nations General Assembly (UNGA) and a diaspora event in Houston, which will also be attended by US President Donald Trump.
( With inputs from IANS )