The delegation from the World Council of Churches and the Christian Conference of Asia urged President Arroyo to order an impartial investigation and ensure the safety of civilians.
They also pushed for a resumption of peace talks between the government and communist rebels to end more than 30 years of Marxist insurgency.
In a statement, the delegation urged the government "to put an immediate end to the pattern of killings that, for many Filipinos, are reminiscent of the Ferdinand Marcos dictatorship."
The 13-member delegation, along with seven Filipino Protestant church leaders, visited northern, central and southern provinces to interview alleged victims of human rights abuses, mostly in areas where the communist insurgency is active.
They did not visit the strongholds of the country’s Islamic separatist rebels, who have made similar accusations.
The Rev. Stephen Sprecher from the United Methodist Church in the United States said they were "deeply concerned by the increase in human rights violations that have occurred during the last few years and in some way, the administration needs to be made accountable."
The conduct of the anti-insurgency campaign is alienating the majority of poor Filipinos from the government, said Bishop Per-Otto Gullaksen from the Church of Norway.
"In its fight against terrorism, the Army seems to be making enemies of the poor people," Gullaksen said.
The leftist human rights group Karapatan recently reported that 411 people have been killed in extra-judicial executions, assassinations and anti-insurgency operations since Mrs. Arroyo took office in January 2001. In addition, 130 people have disappeared after being abducted and 245 others have been tortured, allegedly by government forces, the group said.
Wilhelm Soriano of the government’s Commission on Human Rights said its own investigation showed most victims belonged to left-wing organizations, but it had "not yet validated" that those responsible were members of the military, government militia or vigilantes.
He said it was unfair to compare Arroyo’s administration to the Marcos government.
"There is no basis for comparison because during the Marcos time, it was a dictatorial regime," he said.
He did not disclose any figures for victims. — AP