Chief whip of the BNP in parliament Khandaker Delwar Hossain said the party's decision has been conveyed to the president.
BNP lawmakers attacked Chowdhury for not visiting the grave of Ziaur Rahman, who ruled Bangladesh between 1975 and 1980, on the party founder's 21st death anniversary in May and failing to mention in his official message on the occasion the contribution by Rahman to Bangladesh's war of liberation.
Chowdhury, a former foreign minister in Begum Zia's cabinet, became the head of state in November last year.
He will put in his papers on Friday after attending a family function, his son told reporters.
Chowdhury was a close aide of Ziaur Rahman and was in an adjacent room, in a circuit house in the southern port city of Chittagong on the night of May 30, 1982, when Begum Zia's husband was showered with a hail of bullets.
Ziaur's killing led to another military ruler Gen H M Ershad seizing power.
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