The Russian Navy said Tuesday it was planning to hold war games with the Philippines, as two of its ships made a rare stop in Manila following Filipino President Rodrigo Duterte's pivot from the United States.

Rear Admiral Eduard Mikhailov, the deputy commander of the Russian Navy's Pacific fleet, said the joint military exercises would focus on maritime piracy and terrorism, which he described as the region's two top security concerns.

"We're very sure that in the future we'll get such exercises with you, maybe just the manoeuvreing or maybe use some combat systems and so on," Mikhailov told reporters beside the docked Russian destroyer Admiral Tributs.

Mikhailov also raised the prospect of joint exercises with China and Malaysia in the South China Sea, where competing territorial claims have been a major source of tension and potential conflict for decades.

"We really hope that in a few years, the military exercises for example in your region, in the South China Sea, will (involve) for example, not only Russia-Philippines, but Russia, Philippines, China and maybe Malaysia together."

The visit was only the third ever by Russian military vessels to the Philippines, according to the Filipino Navy's Commodore Francisco Cabudao, who led the welcoming ceremony for the Russian ships.

The Philippines, a former American colony, had for decades been one of the United States' most important and loyal allies in Asia. The two are bound by a mutual defence pact.

But Duterte, a self-described socialist, has during his six months in power sought to dramatically shift his nation's foreign and military alliances towards China and Russia.

Duterte has made repeated threats to downgrade or even end military and diplomatic ties with Washington. He has put on hold the dozens of war games held annually with the United States, and said he wants all American troops to leave the Philippines.

The animosity followed US President Barack Obama's criticism of Duterte's brutal war on drug crime that has left thousands of people dead in the Philippines.

During a trip to Beijing in October last year, Duterte enthused about his plans to forge closer ties with Russia and China.

"America has lost. I've realigned myself in your (Chinese) ideological flow and maybe I will also go to Russia to talk to (President Vladimir) Putin and tell him that there are three of us against the world: China, Philippines and Russia. It's the only way," he said.

Philippine officials have said Duterte is expected to visit Russia in April or May. Duterte has said he is open to the Philippine military holding joint exercises with Russia and China.