The company posted a net loss of 4.44 billion rupees ($88 million) in the three months to December, compared with 2.54 billion rupees in the same period a year earlier.
Sales fell about 25 percent to 13.42 billion rupees from 17.90 billion rupees, while interest charges on its huge debt pile rose to 3.5 billion rupees from 3.4 billion a year earlier.
The company had been due to release figures for its fiscal third-quarter on Tuesday, but it was unable to because of "hardware problems" with its accounting system, it said.
The Bangalore-based carrier, which has seen its passenger market share slump in recent months, is battling a cash-flow crisis that it says was caused by soaring fuel costs and high local sales taxes as well as a domestic price war.
Kingfisher, owned by brewing magnate Vijay Mallya, has never posted a net profit since it started operating in 2005.