"We will continue to resolve the issues on (the Whitsun Reef) through diplomatic channels and through peaceful means," dpa news agency quoted Duterte as saying in a statement.
Defence Secretary Delfin Lorenzana last week asked China to withdraw ships that have been moored on the Whitsun Reef since early March.
The Philippines says the reef sits in its exclusive economic zone, while China says the waters are their traditional fishing grounds.
"Whatever differences we have with China will not define our bilateral relations and will not be an obstacle to the overall positive trajectory of our bilateral friendly relations and our deepening cooperation on pandemic response including vaccine cooperation and in post-pandemic economic recovery," Duterte said.
The President also expressed thanks to China for its donation of 1 million Covid-19 vaccines in March.
The Philippines is banking on China and other countries for the supply of vaccines.
China claims almost the entire South China Sea as its territory and has built artificial islands with military-capable facilities over reefs and outcrops in the area.
Aside from the Philippines, Vietnam, Malaysia, Brunei and Taiwan also have overlapping claims to the area, which is believed to be rich in marine and mineral resources.