The dues which accrued following the implementation of a new pay structure have been pending since January.
The total amount was not immediately available.
ICPA which is the pilots' association of the airlines' narrow body (Airbus A320) fleet had said it will launch an agitation if the payments were not made.
The association had also threatened not to operate flights over the issue.
"The management today paid our flying allowance dues, which it had been defaulting since January," Indian Commercial Pilots Association (ICPA) sources said.
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"We have got written commitment from your office that the flying allowance will be paid on May 5 but looks like the management has gone back to its old feat of defaulting on commitments. This is greatly affecting our livelihood, defaulting on EMI's and further commitments," ICPA had said in a letter to Air India Director (Finance) yesterday.
The association, in the letter had also threatened that "it will not undertake any international flights if the international layover subsistence allowance is not paid by May 10.
