Russell Salic and two others have been charged with involvement in the plan to stage 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 Washington 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 today 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 to help fund 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.
Today the Philippine military chief said Salic had sent funds to other nations for the IS "terrorist network".
"He is providing financial support to several extremists or suspicious terrorists in the Middle East, in the US, Malaysia," Ano told reporters.