Some fled during the mass arrests in the early hours of Sunday morning, but officers rounded up 57 people who they say are homosexual.
Chike Godwin Oti, police spokesman in Lagos state, told the BBC that investigations were continuing and the suspects would be charged.
Homosexual acts are punishable by up to 14 years in jail in Nigeria such relationships were first outlawed under colonial rule in 1901.
Laws were tightened in 2013 when gay marriage and displays of same-sex affection were also banned.
Since then the authorities have cracked down on people suspected of homosexuality. However, arrests are infrequent as homosexual people live in hiding.