The Philippine National Police said it followed the law during simultaneous raids in different provinces in the Southern Tagalog Region that left at least nine activists dead in what rights groups have dubbed "Bloody Sunday."
Charges filed against their targets were "sufficiently supported by evidence," the PNP said. Southern Tagalog police followed operational protocols, it said.
"It was based on verified facts and not on mere membership or affiliation with any organization. The charges of illegal possession of firearms and explosives were sufficiently supported by evidence which served as basis for the issuance of search warrants," the police force said in a statement.
Sunday's bloody raids, which Vice President Leni Robredo had called a "massacre," happened two days after President Rodrigo Duterte told police and military to "kill communists right away" and "ignore human rights."
Former Vice President Jejomar Binay who lost to Duterte in 2016 also reacted to the raids, saying the Philippines has "become a lawless state".
"Activists are not armed combatants. There is a very big difference. And when officials encourage, condone, and even defend the killing of unarmed civilians, there is a clear breakdown in civil governance," he said in a tweet.
The rights body of the United Nations on Tuesday said it was "appalled" by the killings after several local rights groups demanded an independent investigation into the raids.
Following criticism of the raids, the PNP dismissed allegations of evidence planting and abuse of power as "baseless and unfounded," insisting that its operatives "were briefed to exert all possible means to peacefully serve the search warrants."
"The allegations that there was no 'nanlaban' and it was 'planted evidence' are baseless and unfounded. These only serve to undermine the wisdom of the courts and the legitimacy of police operations," the PNP said.
As part of standard procedure, the PNP said its Internal Affairs Service would investigate Sunday's operations.