She also appealed to witnesses and relatives of victims of political violence to come forward with evidence to bring to justice those behind the killings, including soldiers and police officers.
The Melo commission submitted its report to Arroyo on Tuesday but it has not been released to the public.
On Wednesday, Eduardo Ermita, the commission’s executive secretary, said the report was based on initial findings gleaned mainly from military officials and that more needed to be done before the commission could complete its task.
Ermita said the president had asked the justice and defence departments to work with human rights groups and asked the Supreme Court to explore the possibility of organising a special court to hear political killings cases.
The Arroyo government is also asking European human rights officials to work with the investigative panel.
"We will do everything in our power to crack down on political violence leading up to this May elections," Arroyo told diplomats at the Malacanang presidential palace.
Arroyo said rebels were also to blame for the
spate of political killings [GALLO/GETTY]
Without specifying figures, she also said there was a discrepancy between the number of victims of political killings reported by communist "front organisations" and police records.
Jose Melo, a former Supreme Court justice who heads the commission, said on Tuesday that soldiers were involved in a majority of political killings in the country, and that their superiors should be held accountable.
He recommended that commanding officers face military tribunals for extrajudicial killings in their areas because "they should have known what was happening and they just kept silent".
Melo had named retired Major-General Jovito Palparan as one of the commanders who could be held responsible.
Palparan, described as a "butcher" and "executioner" by Karapatan, a local human rights group, has denied any wrongdoing, calling the allegations communist propaganda.
Another rights group, the Bagong Alyansang Makabayan, or Bayan, said the report fell short of "finding the roots of the extra-judicial killings".
It pointed out that killings have continued after Palparan retired, and said there was "a national policy involved which sanctions the assassination of activists".
"The Melo Commission … has shielded the administration from any culpability," it said.
Karapatan has listed more than 800 people allegedly gunned down by security forces since 2001 but it is unclear how many of the cases were investigated by the Melo commission.