“We have rescued the three girls in the early hours of today (Sunday)… in Igbokuta village,” said Lagos State police spokeswoman Dolapo Badmus.
“The girls are in good condition. Some of the suspected kidnappers were arrested when our policemen stormed the location.”
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.
Igbokuta village is some 15 kilometres from the school and about 25 kilometres from Ikorodu.
Police have previously refused to comment on local media reports of demands for a 200-million-naira (nearly $1 million, 900,000-euro) ransom.
Badmus said investigations were continuing and did not rule out further arrests.
Abductions from schools are rare in Lagos, although kidnapping for ransom by armed criminals is common in southern states.