The head of a Philippine office overseeing a bilateral agreement, Zosimo Paredes, met the Marines "to verify that the accused remain in US custody in the Philippines," the embassy said in a statement.
It said the four "are restricted to quarters and they have no official working role at the US embassy."
The statement was in response to local press reports that the four were being allowed to roam freely around a US compound and had been detailed temporarily with a military advisory group.
The mebassy did not say where the four Americans were being confined.
They are accused of raping a Filipina on November 1 after joint military exercises in the former US naval base of Subic, located north of Manila.
Under a visiting forces agreement, providing some legal protection to US troops on official exercises, the US embassy can retain custody of American servicemen pending trial.
However many prominent Filipinos are demanding they be turned over to the Philippines while legal proceedings continue.
The case is being closely followed in this former American colony.
The Americans could face the death penalty if convicted.