The move, second this year, would affect national carrier Air India's flights going to Europe, the US, and Middle East among others.
Flying time of around 50 flights will increase by about 10-15 minutes.
"The major route which we use for our long haul flights are still open and hence the impact is not much right now but we have got initial inputs that the remaining air routes will be shut.
"The impact will be huge as flying time for our ultra long haul flights using Pakistani airspace would increase by 2-3 hours," a senior Air India official told .
The flag carrier had suffered a massive loss of Rs 430 crore due to another air space closure by Pakistan following the Balakot airstrike by the Indian Air Force in February.
The current closure of air space is being seen as retaliation by Pakistan to India's decision ending the autonomy given to the state of Jammu & Kashmir.
On Wednesday, Pakistan downgraded diplomatic ties with India and also suspended trade. It has also told India to withdraw its High Commissioner to Pakistan.
While the air space closure would affect Indian carriers, Pakistan is also expected to take massive financial hit. During the earlier round of air space closure, Pakistan is estimated to have lost about Rs 850 crore in overflying charges from various carriers passing through its territory.
The relations between India and Pakistan has touched a new low since Monday with Pakistani Prime Minister Imran Khan threatening of even a conventional war over the issue of Kashmir.
Following India's move to reorganize Jammu and Kashmir into Union Territories of J&K and Ladakh, Pakistan on Wednesday held a meeting of its National Security Committee to discuss its next course of action to deal with the new developments.
( With inputs from IANS )