The measure will be applied retroactively from April, the company said in a statement, adding the aviation network needs to be maintained as it is essential for Japan's economy.
While Japanese airlines have seen some rebound in domestic flight demand, helped by a government travel campaign, bookings remain below last year's levels.
That means carriers are burning through cash to maintain jets that are either grounded or flying with too few passengers.
Japan's biggest airline, ANA Holdings, said earlier Thursday it was considering revamping its business including reducing its fleet size, as it grapples with a plunge in travel demand due to the Covid-19 pandemic.
A source had told Reuters that ANA was expected to suffer a net loss of around 500 billion yen ($4.8 billion) this fiscal year and cut its fleet of more than 300 aircraft by about 25 to reduce costs.
Separately, the government said last week it would reduce airport landing fees by a record 45% on all domestic flights for seven months through February in government-operated airports, excluding Narita.