Russell Salic and two others have been charged with involvement in the plan to carry out the attacks in the name of the Islamic State group during the Muslim holy month of Ramadan in 2016.
Salic was arrested in the Philippines in April 2017 and the US had requested his extradition, the US Department of Justice said.
"It only means that we have to begin the extradition proceedings being requested," Philippine Justice Secretary Vitaliano Aguirre said in a statement without giving a timeframe.
The Philippine military chief, General Eduardo Ano, said on Sunday that Salic was in the custody of the country's National Bureau of Investigation.
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Salic, a 37-year-old Filipino doctor, transferred USD 423 in May 2016 to the other suspects for the operation, according to US court documents released on Friday.
Multiple locations including New York's subway, Times Square and some concert venues were identified as targets in the plot that was foiled by an undercover FBI agent, US authorities announced Friday.
The agent posed as an IS supporter and communicated with Salic and his two alleged accomplices: Abdulrahman El Bahnasawy, a 19-year-old Canadian who purchased bombmaking materials, and Talha Haroon, a 19-year-old American citizen living in Pakistan.
Salic was an orthopaedic surgeon associated with a hospital in the southern Philippine city of Cagayan de Oro, the complaint said.
The restive south of the mainly Catholic Philippines is home to a decades-old Muslim separatist insurgency and extremist gangs that have declared allegiance to IS.
Today the Philippine military chief said Salic sent funds to other nations for the "IS terrorist network".
"He was very active on social media, websites that groups related to ISIS have been using," Ano said using another name for IS.
Authorities had been monitoring Salic's activities since 2014, Ano added.