Judge Marcel Montalvao in the small northeastern town of Lagarto issued the order because Facebook, the owner of the service, failed to hand over information requested in a criminal investigation, reported news site G1.
The judge "has ordered the suspension of WhatsApp from 2:00 pm (1700 GMT) Monday," a court spokeswoman told AFP.
WhatsApp was previously shut down in Brazil in December over a similar dispute, before a higher court threw out the two-day suspension after about 12 hours.
WhatsApp is widely used in Brazil, where cell phone fees for texting and calls are among the highest in the world.
The free app is installed in nine in 10 smartphones in the country.
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