In an attempt to boost negotiations, Duterte last year freed top rebel leaders from prison and met them at the presidential palace, but the peace process quickly soured after deadly attacks against soldiers and police angered the president.
Duterte signed an order Tuesday declaring two communist groups "terrorist organisations", but it would require court approval to go into effect, his spokesman Harry Roque told reporters.
The classification targets the Communist Party of the Philippines (CPP) and its 3,800-member armed wing, and the New People's Army (NPA), accusing them of "continued violent acts".
The Tuesday order follows a 2002 US classification of the two groups as "foreign terrorist organisations".
Communist rebels have been waging an insurgency in the Philippines since 1968 to overthrow what they call a capitalist system that has created one of Asia's biggest rich-poor divides.
Peace talks to end the conflict -- which the military says has claimed 30,000 lives -- have been held on and off for three decades.
Duterte's election last year revived hopes for successful negotiations as the president is a self-declared socialist who has said it is his "dream" to forge peace in the country.
But he cancelled peace talks in November after a rebel ambush in the southern Philippines killed a police officer and a four-month-old baby.
Duterte has also accused the communists of plotting with his political rivals to destabilise his rule.
He has since ordered the arrest of more than a dozen rebel leaders freed last year, and has threatened to shut down mining companies that yield to insurgents' demands for money.
Roque said Tuesday's order would allow the military and the police to crack down on people funding the rebels.
The military said the declaration would also make its operations against the insurgents "more effective".
"We can now address without any hesitation and with all the means and resources available to us the increasing criminal and economic sabotage activities of these terrorists," military spokesman Major-General Restituto Padilla said.
Chief rebel negotiator Fidel Agcaoili of the National Democratic Front -- a group linked with the communist rebels but not targeted by Duterte Tuesday -- denied that the NPA was a terrorist group.
But he said the communists would not question the declaration in court.
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