A letter signed by the country's bishops will be read out at all services.
In it they say killing people is not the answer to tackling the country's drug problem.
The letter, without naming the President, suggests a "reign of terror" has been brought about among the poor due to the extreme crackdown which is said to have seen more than 7,500 people killed.
When President Duterte took office last year he promised to strongly deal with the drug issue and police have said a number of shootouts have taken place during raids and sting operations.
According to Reuters, the Catholic Bishop's Conference of the Philippines will say: "An additional cause of concern is the reign of terror in many places of the poor."
"Many are killed not because of drugs. Those who kill them are not brought to account."
The President's office is yet to comment on the bishops' letter.