"The victim has been traced. She was staying at a woman friend's house in Mapusa town," a police spokesperson told reporters. Mapusa town is located a short distance from the state capital.
The girl in 2016 had accused Congress leader Atanasio Monserrate, contesting the Panaji by-election, of sexually assaulting her.
Chief Minister Pramod Sawant has congratulated the Goa Police for tracking her down, whose disappearance had triggered controversy in the run-up to the vote.
"I congratulate the Goa Police team for tracing the missing victim girl. Women safety is topmost priority of our government," Sawant tweeted.
On April 28, nuns who run the rehabilitation home in South Goa had filed a missing complaint after she disappeared. Later, the police registered a first information report (FIR) under section 362 (abduction) of the Indian Penal Code.
Monserrate was charge-sheeted last year under Section 376 of the Indian Penal Code and Section 506 of the Protection of Children from Sexual Offences Act after being booked in 2016 for allegedly raping the girl, who was minor at the time, after drugging her.
The Congress blamed the disappearance of the victim on the poll-eve on the BJP, calling it an attempt by its "dirty tricks" department to influence voters against Monserrate.