While 22 flights of the airline were cancelled from Delhi, nine were cancelled from Mumbai, sources said.
A section of its employees, including pilots and engineers are not reporting for work to protest non-payment of salary, they said.
Meanwhile, the board of the near-bankrupt airlines is meeting in New Delhi today to discuss finances ahead of the announcement of quarterly results.
"The airlines' board is meeting at a five-star hotel in south-west Delhi this afternoon to discuss finances," the sources said.
The airline's operations have been disrupted time and again since April when pilots called off work protesting salary delays.
Kingfisher Airlines, which has been facing fund-crunch for almost a year now, has not paid a salary to its staff for the past five months. A sizeable number of its employees have not been paid since February.
"We just can't work without being paid for such a long time. Hence the decision (to strike work)," a pilot has said.
The decision of airline employees to go on agitation coincides with the monsoon session of the Parliament that starts today.
"We hope that the strike will pull the attention of Parliament and our plight and misery echoes in political corridors," an employee said.