The investigation began about three days ago and culminated with an arrest hours after a local woman came forward.
Millbrook Police chief Kenneth Bradley confirms his office took a call at about 2:30 Friday morning from doctors at Prattville Baptist Hospital.
A woman there told medics she was raped - and that her attacker was a Millbrook officer.
Chief Bradley says at that point, he asked Elmore County deputies to take over the investigation.
They interviewed the woman and the doctors, and agreed they had enough evidence.
Investigators then asked for an arrest warrant.
The took 36 year old Francisco Aponte into custody, charged him with rape first degree and took him to the Elmore County jail.
Chief Bradley says the city fired Aponte immediately after his arrest, and now, Bradley cannot comment further on the case.
Aponte used to live in Montgomery and state records show he worked for Alabama State University before taking the Millbrook Police job.
A district judge set a high 150-thousand dollar bond for Aponte. He made bail the same day. The court has not set a date for his arraignment.
WSFA 12 News and wsfa.com will keep you updated.