The Philippines and Japan have long been key US allies in Asia, but Duterte has done a dramatic U-turn since coming to office in late June.
That appeared to culminate last week in Beijing where he declared his "separation" from the United States, played down a maritime dispute with China and pledged to enhance friendship and economic ties.
Back home on Saturday, however, the former mayor seemed to walk back his comments, saying he would not be severing the alliance with Washington.
"The alliances are alive, it is there," he said in a reference to the United States, according to Kyodo News.
"There should be no worry about changes of alliances. I do not need to have alliances with other nations."
Other Japanese media including the top-selling Yomiuri Shimbun quoted him as saying that all military activities with the US should be halted.
His seesawing has been closely watched in Japan, a major investor and aid donor to Manila that is wary of China's rising influence.
Prime Minister Shinzo Abe has worked to beef up relations with Manila by providing patrol boats and has supported it in the territorial row with China, as Japan seeks support in its own maritime dispute with Beijing.
Duterte's predecessor took Beijing to an international tribunal over its extensive claims in the South China Sea -- where it has built artificial islands capable of hosting military facilities -- and the Philippines won a resounding victory in July.
"But if they disrespect the rule of law for the sake of narrow bilateral interest, that would be a grave concern for the Asian region," it said in a Saturday editorial, referring to Duterte's Beijing visit.
Duterte told Japanese public broadcaster NHK that his talks with Abe will centre on economic cooperation and "shared interest" in an interview ahead of his three-day visit.
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