Police raids dubbed 'One Time Big Time' saw at least 76 people shot dead, authorities said, as rights groups and lawmakers condemned the operation as an alarming "killing spree" in the Philippines.
On Sunday, the highest-ranking Catholic official in Asia's only predominantly Christian country expressed concern about the increase in the number of deaths.
In a statement read in Sunday Masses in the capital, Cardinal Luis Antonio Tagle said: "We knock on the consciences of those who kill even the helpless, especially those who cover their faces with bonnets, to stop wasting human lives.
"The illegal drug problem should not be reduced to a political or criminal issue. It is a humanitarian concern that affects all of us."
President Duterte has launched an unprecedented crackdown on illegal narcotics since winning the presidency last year on a promise to kill thousands of criminals.
The Roman Catholic Church, which is one of the nation's oldest and most influential institutions, has been among the few voices denouncing the deaths.
Police officials have confirmed that they have killed more than 3,500 people since President Duterte was elected 14 months ago. They have insisted they acted in self-defence.
More than 2,000 other people have also been killed in drug-related crimes and thousands more murdered in unexplained circumstances, according to police data.
This week alone, officers shot dead 32 people in a single province prompting praise from the President.
Cardinal Tagle called for nine days of prayer for people who have died in the drug war.
He said: "Those with sorrowful hearts and awakened consciences may come to your pastors to tell your stories and we will document them for the wider society."
The president of the Catholic Bishops' Conference of the Philippines also denounced the deaths, calling on the faithful to ring church bells daily in solidarity with the victims.
Archbishop Socrates Villegas said in a statement: "The sound of the bells is a wake-up call for a nation that no longer knows how to condole with the bereaved, that is cowardly to call out evil.
The sound of the bells is a call to stop consenting to the killings."
