The canceled flights included those to and from Shanghai, Beijing, Taipei, Dubai, Delhi, and Dhaka, Hong Kong Standard reported.
The flagship carrier said more pilots have been absent due to seasonal illness, and so it has been cutting a small number of passenger flights, less than 1% of the total, since mid-December.
Cathay canceled at least 16 flights, including long-haul ones to London and Amsterdam over the Christmas holiday.
Then, an additional 28 were suspended in the run-up to New Year's Eve.
"Our operations remain normal overall, with a marked increase in the number of flights operated over the holiday peak season," Bloomberg reported citing a source from Cathay.
Cathay apologized to customers affected by the mass cancelations and said it will do everything it can to minimize the disruption.
According to the Hong Kong Aircrew Officers Association, Cathay had 2,532 pilots as of December last year, compared with 3,885 in the fourth quarter of 2019.