Prayers, penance and fasting are held on Good Friday to commemorate the crucifixion of Jesus Christ 2,000 years ago.
The ruling Congress-led Meghalaya United Alliance government has decided not to participate in the programme.
The opposition Hill State People's Democratic Party and National People's Party have also opposed the Centre's move.
Meghalaya Chief Minister Mukul Sangma said his government will not participate.
"Is it that they selectively identifying these dates to marginalise the minorities with a complete disregard to the constitutional obligation of ensuring personal liberty?" the Congress leader asked.
It is a part of a mega draw and 'Digi Dhan' planned for April 14 for the promotion of digital payments in 100 cities across India. The list does not include Nagaland, Kumar said.
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