SpiceJet paid up Rs 22 crore, while Jet made a payment of Rs 80 crore, official sources said.
Jet owes AAI a total of Rs 165 crore and SpiceJet a total outstanding of Rs 119 crore.
The sources said SpiceJet has paid another Rs 15-18 crore earlier which was not accounted for then.
At a meeting earlier this week, the two airlines had informed the AAI about their readiness to settle part of their outstanding as the airports body threatened penal action if the dues were not settled by month-end.
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As per official figures three months ago, five private airlines, including Kingfisher Airlines which went bust, have over Rs 350 crore as dues pending towards AAI. Of this, the Vijay Mallya-owned airlines alone owes Rs 186.26 crore.
AAI has taken the litigation route against Kingfisher and Paramount Airways, which has also closed down, to realise its pending dues.
The dues of private carriers are monitored on regular basis and in case of delay, the AAI issues notices to the airlines for their settlement.