The United States said the Philippine government had not officially communicated President Rodrigo Duterte's demand to pull US military advisers out of the rebellion-torn southern Philippines.
Since 2002, up to 600 US advisers have been deployed in the Mindanao region to train troops battling Muslim extremists but their numbers have been scaled down in recent years.
Duterte said on Monday that US Special Forces in the region "have to go".
Foreign Secretary Perfecto Yasay however attempted to downplay Duterte's comments, saying on Tuesday they were "in the context of wanting to save the lives of these Americans who might be exposing themselves to unnecessary risk" from militant attacks.
In Washington, the Pentagon and State Department said they had not been officially contacted by Manila about pulling out the remaining advisers.
Yasay, interviewed by Manila's ABS-CBN network, also confirmed the allies had not discussed Duterte's demand.
He said only around 100 US advisers were left in the south of the country.
The Pentagon in June also deployed warplanes and about 120 personnel in the northern Philippines for short-term training missions aimed at ensuring the allies' access to the disputed South China Sea.
Duterte, 71, has said he is "not a fan" of the United States and on Monday explained his demand by showing pictures of US troops killing Muslims as America took control of its new colony in the early 1900s.
He has said the spat was triggered by State Department criticism of his controversial war on drug crime, which has left about 3,000 people dead since he began his six-year term on June 30.
Obama has said Duterte must conduct his crime war "the right way", protecting human rights.
Yasay stressed that Duterte's new comments did not signal a shift in policy, and that ties with the US remained strong.
The president only wanted to protect Americans from kidnappings and terrorism as they had become "a very good target", Yasay said.
"There is no shift in so far as our policy is concerned with respect to our close friendship with the Americans."
Yasay, who was heading to Washington for talks, added the Duterte administration would honour existing defence agreements including a 2014 accord giving the US military access to at least five Philippine bases, one of them in Mindanao.
Duterte's spokesman Ernesto Abella also said on Tuesday the president's pronouncements were not to be taken as policy.
"These were not directives to leave, OK? But this was a context on why we have a conflict (in Mindanao). In other words, he's giving a broad historical, cultural landscape."
However, analysts said any drawdown would could come at a time of deteriorating security in Mindanao, with the presence of extremist and splinter rebel groups, some of which pledged allegiance to the Islamic State group.
Zachary Abuza, a Southeast Asian security expert at the National War College in the United States, said Duterte's actions towards the US were worrying.
"National security professionals that I am in contact with are agog with the behaviour of a treaty ally," Abuza told AFP.
"It is going to take a lot of work to get this relationship back on track."
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