In a letter to the Philippine government, the US embassy invoked the bilateral Visiting Forces Agreement, which allows large-scale US training in the country, and vowed to keep the marines in its custody during an upcoming trial.
Prosecutor Prudencio Jalandoni said he was disappointed but would ask the court handling the rape case to abide by the US decision and set a trial date.
Custody of the Americans “is important for the purpose of showing that we are a sovereign and independent state, but... what is important to us is that justice be done,” Mr Jalandoni said.
A Philippine judge last week issued arrest warrants for the marines, who were charged with rape late last year while on liberty following counter-terrorism manoeuvres with Filipino troops.
Prosecutors allege that Lance Cpl Daniel Smith raped a 22-year-old woman on November 1 inside a van at Subic Bay, a former US Naval base north-west of Manila, as fellow marines cheered him on. Smith claims he only had consensual sex.
Also charged were Lance Cpl Keith Silkwood, Lance Cpl Dominic Duplantis and Staff Sgt Chad Carpentier, part of the 31st Marine Expeditionary Force stationed in Okinawa, Japan.
The case has stirred emotions in the former American colony and is seen as a black mark on US military exercises, which have been credited with helping to weaken al-Qaida-linked militants in the country’s restive south.