This was a reversal of the rebels earlier position that they would not attack American troops helping in relief efforts.
The deployment of US forces from Feb. 21 to March 6 is part of annual military exercises aimed at promoting compatibility of US and Filipino troops for possible security contingencies.
Col. Mathias Velasco, chief of the Joint US Military Advisory Group, earlier said a number of US troops will join nearly 700 Filipino troops to bring humanitarian help to Quezon, one of the provinces hit hardest by successive storms and typhoons late last year.
More than 1,600 people died, mostly in landslides and flash floods blamed on unabated illegal logging.
The troops will construct new school buildings and provide medical and dental services to communities in nearby Laguna province, officials said.
Rebel spokesman Gregorio Rosal said, however, the relief operations could be a pretext for American troops to intrude into rural NPA strongholds in the two provinces to spy and help crush the Marxist rebel movement.
"An increasing number of US combat troops and spies are directly interfering in the armed conflicts in the Philippines," Rosal said in a statement. "These constitute escalating US military intervention and are a blatant mockery of Philippine sovereignty."
NPA forces are "ready to fight US combat troops that help the (military) trample on human rights and kill Filipinos," Rosal said.
Philippine military officials have denied the rebel allegations.
Late last year, Rosal promised that US troops helping in the aid efforts would not be attacked.
His announcement came after the NPA suffered a public relations setback when a rebel band ambushed an unarmed Philippine Army unit bringing aid to typhoon victims. At least 10 soldiers were killed.
The guerrillas, estimated by the military to number 8,240, have been waging a Marxist insurrection for more than three decades and are on a US and European Union watch list of terrorist organizations.
The rebels suspended the last round of Norwegian-hosted peace talks in August to protest Manilas refusal to pressure the United States and the European Union to remove them from the terror list.
All funds and assets of groups on the list are frozen by the United States and the European Union. Benjie Villa, James Mananghaya