Russell Salic and two others have been charged with involvement in the plan to stage the attacks in the name of the Daesh 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.
“We have a process to be followed and this has been done many times in the past.”
The Philippine military chief, General Eduardo Ano, said on Sunday that Salic was in the custody of the country’s National Bureau of Investigation.
Salic, a 37-year-old Filipino doctor, transferred $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.
A complaint signed by the agent quoted messages sent by Salic to others involved in the plot in which he described terror laws in the Philippines as “not strict” in comparison to countries such as Australia and the UK.
Salic was an orthopedic surgeon associated with a hospital in the southern Philippine city of Cagayan de Oro, the complaint said.
On Sunday 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.
“He was very active on social media, websites that groups related to ISIS have been using,” Ano said using another name for IS.
Salic is also under investigation in the Philippines over kidnapping and murder charges and those probes will continue pending a decision on the extradition proceedings, the presidential palace said.
“The Philippines shares information and extends full cooperation with partners on matters pertaining to terrorism,” presidential spokesman Ernesto Abella said in a statement.
The restive south of the mainly Catholic nation is home to a decades-old Muslim separatist insurgency and to extremist gangs that have declared allegiance to IS.
Armed militants flying the black IS flag have been besieging the southern city of Marawi since May, leaving more than 950 people dead.
The fighting, which is still raging despite artillery and air strikes and US military assistance, has left the once-thriving city in ruins and thousands of civilians displaced.