Members of Inglesia ni Cristo (Church of Christ) have been lining the streets of the capital Manila because the country's Justice Department, led by Ms Leila de Lima, is investigating allegations that some of denomination's members have been kidnapped and detained against their will.
Inglesia ni Cristo denies the claims.
Local media have reported that Inglesia ni Cristo protestors began the demonstration on Thursday by marching to the Philippines Justice Department and stopping Ms de Lima's car from leaving the premises.
They have been calling for her resignation, and for the government to uphold the separation between church and state.
A spokesman for the government told Reuters it "does not wish to interfere in the internal affairs of any legitimate organization."
Around eight in ten Filipinos identify themselves as Catholics, with Muslims and Christian groups making up most of the remaining people.
The largest denomination outside of the Catholic Church in the Philippines is Inglesia ni Cristo.
