Three flights from Mumbai and several across the airline's entire network were cancelled.
An airlines spokesperson said, "A certain section of employees have decided to stay away from duties due to salary payments not being credited to the bank accounts of all employees by Friday. Kingfisher wishes to state that more than 75% of employees have actually received their promised salaries on Friday."
"We have further promised that the balance of our employees will receive their salaries by Monday", the spokesman said.
The passengers booked on these flights have either been re-booked or given refunds, he said.
The strike on July 2 was called off after a few hours with the management promising to pay some sections of staff from July 6.
A large number of its flight engineers have reportedly quit over the past five months, primarily due to delayed payments. In April, around 200 engineers reported sick as a mark of protest over the issue.
The airline, which has not posted profit since inception in May 2005, has reported a loss of Rs 1,151.50 crore in the March quarter, has a debt of over Rs 7,500 crore and almost an equal amount of accumulated losses.