“We met with the campaign organisers on Monday and we have all agreed that the campaign should be stopped,” the ministry’s disease control and environmental health chief, Tjandra Yoga Aditama, told reporters on Wednesday.
Tjandra said the ministry had only given approval for the event; it was not handling its implementation.
National Condom Week is an annual event that was launched in 2007.
The campaign sparked controversy following a publicity stunt published for the event.
One of the programme’s advertisements included posters on a city bus showing actress and singer Julia Perez in a sexy pose along with the National Condom Week 2013 logo.
Members of conservative groups said the posters could encourage promiscuity among young people.