The government stopped the subsidy for the annual pilgrimage "abruptly". The Supreme Court had in 2012 said the subsidy should be phased out over 10 years, it said.
"The sudden withdrawal of the subsidy seems arbitrary and motivated by other considerations," a party statement read.
The CPI(M) asserted it never supported "state subsidy or funding of pilgrimages".
After this move, there should be no "central or state government funding" for subsidies and grants for pilgrimages, it said.
Minority affairs minister Mukhtar Abbas Naqvi yesterday announced the scrapping of the subsidy for Haj from this year, four years ahead of a deadline suggested by the apex court in a 2012 order.