Under the law, which was passed by parliament last year but doesn't come into effect until 1 July, church ministers and the country's Head of State will have to pay income tax for the first time.
The Catholic Church and the Methodist Church have said that they accept the law and that their ministers will pay the tax. The Head of State will also pay.
But at a recent general assembly, the leaders of the Congregational Christian Church said they would flout the law, arguing that the payment of income tax goes against their faith.
The Congregational Church is Samoa's largest, with 29 percent of Samoans identifying with it, according to the 2016 census, giving it a certain degree of societal heft - although no real legal authority - in a deeply religious country.
But the church's general secretary, Reverend Vavatau Taufao, said the new law was seen by the assembly as an affront to their beliefs because many pastors lived off donations.