State-owned Indian Airlines and the private carrier Jet Airways will begin the extra flights from Thursday, a government statement said.
A number of Arab countries, including Saudi Arabia and Egypt, have cut diplomatic ties with Qatar, accusing it of destabilising the region.
Indians are the largest group of migrants in Qatar.
The move came after India's Aviation Minister Ashok Gajapathy Raju held talks with Foreign Minister Sushma Swaraj, and assured her that additional flights would be operated to allow Indians who had been unable to book tickets, to return home.
The government statement said Air India would run extra flights between the southern city of Trivandrum and Doha from 25 June to 8 July while Jet Airways will operate Mumbai-Doha-Mumbai flights on 22 and 23 June.
Two airlines will start operating extra flights to Doha, the Qatar capital to help stranded Indians return home.