"The increase in extrajudicial executions in recent years is attributable, at least in part, to a shift in the military's counter-insurgency strategy," Alston, the UN's special rapporteur on extrajudicial killings, told a news conference in Manila, the capital.
"In some areas, an appeal to hearts and minds is combined with an attempt to vilify left-leaning organisations and to intimidate leaders of such organisations.
"In some instances, such intimidation escalates into extrajudicial executions."
He said that many of the killings had been "convincingly attributed" to the military, which he said was in "almost total denial".
He added that there was a "problem of virtual impunity" which meant that eight out of 10 cases failed to move from police investigation to prosecution.
Karapatan, a local rights group, has said that more than 800 people, mostly left-wing activists, have been murdered or reported missing since Arroyo came to power in 2001.
But the military says most of the deaths could be attributed to internal fighting in the New People's Army, a communist rebel movement.
Alston, an Australian lawyer, said he did not know how many had died, but added: "I am certain the number is high enough to be distressing.
"The impact of even a limited number of killings of the type alleged is corrosive in many ways.
"It intimidates vast numbers of civil society actors, it sends a message of vulnerability to all but the most well-connected, and it severely undermines the political discourse which is central to a resolution of the problems confronting this country."
Alston's comments have not gone down well with the government.
"It is not national policy to conduct extrajudicial executions," said government spokesman Eduardo Ermita.