"From midnight to the early hours today we were able to rescue them," Lagos State police spokeswoman Dolapo Badmus told AFP.
The three girls were seized from a dormitory last Monday at the Babington Macaulay Junior Seminary School in the eastern suburb of Ikorodu.
The abduction sparked a massive search for the teenagers and the prompted the state government to tighten security at schools across the megacity, which is home to some 20 million people.
No further details were immediately available and police have previously refused to comment on local media reports of demands for a 200-million-naira (nearly USD 1 million, 900,000-euro) ransom.