Details about the amount paid as allowances could not be immediately ascertained.
Air India has around 1,600 pilots and all of them have received the payment, he said.
Last week, the government provided a Rs 500-crore guarantee to the national carrier to help it secure fresh funds for operational requirements.
This was against a request for Rs 2,400 crore sovereign guarantee for raising funds.
According to the government, it has infused funds to the tune of Rs 30,520.21 crore in the flag carrier from financial year 2011-12 till Dec 5.
The Indian Commercial Pilots Association (ICPA), a grouping of the carrier's pilots who operate narrow-body planes, had demanded clearing of their legitimate dues without any delay.
"We have never received our salaries and flying allowance on time, in the recent past 2-3 years. Flying allowance constitute 70 per cent of pilots pay package and we are facing severe financial constraints due to delay in (payment of) flying allowance," the grouping said in a letter, dated December 23, addressed to Minister of State for Civil Aviation Hardeep Singh Puri.
The source said flying allowance of the senior-most pilots account for 80 per cent of their salaries while at the mid-level this allowance is 70 per cent.
For the junior-most pilots, the ratio of the salary and flying allowance is 50:50.
As the government works out the modalities for the sale of the national carrier, ICPA had also warned that they are in no position to work amid uncertainty over the airline's future.
Recently, Puri said that Air India would have to shut business if it is not privatised.
Air India's net loss in 2018-19 is provisionally estimated to be Rs 8,556.35 crore and its debt stands over Rs 58,000 crore.
The Air India Specific Alternative Mechanism (AISAM) has approved re-initiation of process for the the government's 100 per cent stake sale in Air India along with Air India Express and the carrier's stake in joint venture AISATS.
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