The crackdown in the Muslim-majority nation has prompted fears that the traditionally tolerant country is taking an increasingly fundamentalist turn.
New laws have recently been introduced which could see pre-marital (including homosexual sex) criminalised and punishable with imprisonment.
Authorities in Indonesia's second-largest city, Surabaya, briefly detained roughly two dozen couples on Valentine's Day.
Although the couples are expected to released with a reprimand, tourists in the popular resort of Mataram on the island of Lombok will need to be more careful, where police have even been ordered to raid schools to hunt for passionate students.
However, romantic parties at hotels and cafes were left alone, according to authorities.
Valentine's Day "has never been declared by the government to be a celebration in the country" and the ban would prevent illicit encounters among students, said Syamsu Rizal, the deputy mayor of Makassar on the island of Sulawesi.
Makassar has prohibited Valentine's Day for several years, and last February police raided shops to confiscate condoms to prevent teenagers from having sex.
"Valentine's Day reflects a culture which is not in line with [the city of] Aceh's and Islamic law," provincial governor Irwandi Yusuf said in a statement.
Clerics and conservative Muslims in Indonesia have criticised Valentine's Day as an example of Western decadence.
However, many Indonesians continue to practise a moderate form of Islam and celebrate the romantic holiday with cards, chocolates and flowers for their loved ones.
