The London-based human rights watchdog made the appeal even as it lauded Mrs. Arroyo for ordering an investigation into the violence of recent years.
Amnesty urged the President to make "a public statement to make it crystal clear to all — including the Armed Forces of the Philippines (AFP), the Philippine National Police (PNP) and other security forces — that their involvement in such killings will not be tolerated and that she will do everything in her power to combat impunity."
Last week, human rights group Karapatan said it had documented the killings of 73 leftist activists by suspected government forces or their agents so far this year, and 152 in 2005.
Karapatan claimed more than 140 left-wing activists had been abducted and remain missing since Mrs. Arroyo took office in 2001, and almost 600 were killed during the same period.
At least 79 journalists have been killed since democracy was restored to the country in 1986, according to the National Union of Journalists of the Philippines (NUJP).
The government and military have denied any involvement in the killings and abductions.
Press Secretary and Presidential Spokesman Ignacio Bunye has said the government is proud of its human rights record.
The communist New People’s Army (NPA), in a statement, vowed to punish what they called "Black Army" death squads — alleged shadowy assassins directed by military officers and a Cabinet security committee to kill government critics.
"Those principally responsible for the series of political killings will be made to answer for their fascist crimes," rebel spokesman Gregorio Rosal said.
Former President Joseph Estrada warned the government of rising public fury against "a government that violates all fundamental rules and where the military is no longer the protector of the people but their tormentor."
In its statement, Amnesty said Mrs. Arroyo "must also go the extra mile to make it absolutely clear that this government will not shirk from its responsibility to protect the individuals at risk — whether journalists, leftist activists or those suspected criminals.
"Any forces operating outside the chain of command but with the acquiescence of any official should be immediately prohibited and disbanded," Amnesty International said, adding that those "who have perpetrated extra-judicial executions should be brought to justice."
Among the most recent killings, former communist rebel leader Sotero Llamas was shot dead Monday in an ambush in Tabaco, Albay.
Two days earlier, gunmen killed Noli Capulong, a member of the left-wing Bayan Muna party list organization.
Activists have blamed security forces for both killings. Military officials said communist rebels could be to blame in carrying out internal purges among their ranks.
The spate of killings of leftist leaders prompted the government to form Task Force Usig with Interior and Local Government (DILG) Secretary Ronaldo Puno to head the investigating body.
Malacañang said anyone suspected of involvement in the killings should be investigated and charged, even those from the government.
Officials expressed concern over the spate of killings which they called "anathema to our democratic system." — AP, Katherine Adraneda