President Rodrigo Duterte claimed over the weekend he was not aware prior to the fact that the US government was providing assistance to government troops in its battle against Islamist militants in the Islamic City of Marawi.
Duterte, who has made a series of rhetorical attacks against the USA - the Philippines longest-standing military ally - retracted his statement that the southern Philippines "would never have peace" while allied with Washington.
It is unclear whether the pro-American military went over Duterte's head in seeking USA help.
In a statement provided to Defense News, a U.S. Special Operations Command Pacific spokeswoman said, "U.S. special operations forces are assisting the AFP with ongoing operations in Marawi that helps AFP commanders on the ground in their fight against Maute and ASG militants" at the request of the Philippine government.
Indonesia says it was looking to set up joint patrols with the Philippines and Malaysia to prevent Islamic militants who have laid siege to Marawi.
The embassy told CNN it would not provide further details about the USA support due to "security reasons," but added US special operations forces have provided assistance in response to Philippine military requests for years.
The ultra-radical group's news agency, Amaq, said the military in the largely Christian Philippines had "completely failed" to take back Muslim-majority Marawi.
Speaking on condition of anonymity, a USA official said support included aerial surveillance and targeting, electronic eavesdropping, communications assistance and training.
According to local media reports, a US P-3 Orion surveillance plane was seen flying over the town on Friday.
Philippine President Rodrigo Duterte has declared martial law across a large southern portion of his country.
The United States troops are reportedly helping the Armed Forces with the operations in Marawi in the areas of surveillance and intelligence.
Their plot was foiled because troops made a preemptive raid on Marawi to capture Isnilon Hapilon, leader of the Abu Sayyaf group and Islamic State's "emir" of Southeast Asia.
"Secretary Cayetano and Prime Minister Abe had fruitful discussions on the state of Philippines-Japan relations and highlighted the friendship between Prime Minister Abe and President Duterte", the DFA said. "The Philippines is open to assistance from other countries if they offer it".
At least 58 soldiers and police have been killed in Marawi City. The death toll for civilians was 20 and more than 100 had been killed overall.
Outside governments have expressed alarm over the siege by the militants, who are still holed up in buildings with civilian hostages in Marawi's commercial district. An estimated 500 to 1,000 civilians are trapped there, some being held as human shields, while others are hiding in their homes with no access to running water, electricity or food.
He also said the Maute Group plotted to also attack Iligan City and kill as many people as they can.
Maute joined forces with Isnilon Hapilon, who was previous year proclaimed by Islamic State as its Southeast Asia "emir".
Former military chief Rodolfo Biazon told ABC-CBN television on Monday that the government seemed to be struggling to control the situation because rebel forces could move freely in an out of the town, raising the prospect of reinforcements.