Many in the Government have concluded that numerous civil society organizations are "fronts" for the Communist Party of the Philippines (CPP) and its armed group, the New People's Army (NPA). One response has been counter-insurgency operations that result in the extrajudicial execution of leftist activists. In some areas, the leaders of leftist organizations are systematically hunted down by interrogating and torturing those who may know their whereabouts, and they are often killed following a campaign of individual vilification designed to instill fear into the community. The priorities of the criminal justice system have also been distorted, and it has increasingly focused on prosecuting civil society leaders rather than their killers.

The military is in a state of denial concerning the numerous extrajudicial executions in which its soldiers are implicated. Military officers argue that many or all of the extrajudicial executions have actually been committed by the communist insurgents as part of an internal purge. The NPA does commit extrajudicial executions, sometimes dressing them up as "revolutionary justice", but the evidence that it is currently engaged in a large-scale purge is strikingly unconvincing. The military's insistence that the "purge theory" is correct can only be viewed as a cynical attempt to displace responsibility.