In the meeting that lasted 30 minutes, the two are understood to have discussed the ongoing crisis.
Jet Airways and its subsidiary JetLite were forced to cancel at least 10 flights out of Delhi following the protest. Ministry officials said the government was closely monitoring the situation.
The National Aviators Guild (NAG) has decided not to go on a strike and its members decided alternate course of protest action like going on mass casual leave, which hampered the operations of the private carrier.
The union, which gave a strike call from midnight on Monday, had termed the sackings "an act of vendetta" and demanded the reinstatement of the pilots.
Jet Airways had last month terminated the services of two of its senior-most pilots, saying, "Their services were not required" after they along with others formed a trade union body in the company.