President Rodrigo Duterte has decided to retain the Philippines' security alliance with former colonial power the United States, according to the country's defense minister, but joint military activities will be scaled back and less combat-focused.

Duterte has threatened repeatedly to cut defense pacts and end joint drills involving thousands of soldiers, after lashing out at criticism by the Obama administration of his war on drugs, which has claimed more than 2,300 lives in four months.

But Defense Secretary Delfin Lorenzana said the security alliance with the United States would not be scrapped, including a 2014 agreement that allows prolonged deployment of American forces in the country.

"It will remain," Lorenzana told reporters, referring to the strategic alliance with Washington. "No, it will not be abrogated. But we will reduce the number of activities."

However, naval exercises known as CARAT, or cooperation afloat readiness and training, and Phiblex, a marine amphibious landing exercise, would be ditched, he said. Both have been held annually.

Lorenzana said the war games called Balikatan (shoulder-to-shoulder), involving thousands of American and Filipino soldiers and marines, would continue but be re-focused on humanitarian, engineering and civic action activities.