The court in Sao Paulo state made the order because it said WhatsApp had repeatedly failed to co-operate in a criminal investigation.
It is not clear if mobile companies will fully comply with the order.
Facebook owns the app. Mark Zuckerberg said he was “stunned” by the “extreme” ruling.
WhatsApp is reported to be the most used application in Brazil, with about 93 million users.
According to the TechCrunch website, WhatsApp is used by 93% of Brazil’s internet population and is especially popular among young people and the poor who take advantage of its free text message and internet telephone service.
It says Brazilians spend almost twice as much time on social media as Americans.
Brazilians have taken to Twitter to express their anger at the suspension but also to joke about how dependent they have become on WhatsApp.
WhatsApp CEO Jan Koum said he was “disappointed in the short-sighted decision to cut off access to WhatsApp, a communication tool that so many Brazilians have come to depend on, and sad to see Brazil isolate itself from the rest of the world”.
Mark Zuckerberg was also highly critical of the ruling.
He wrote on his Facebook page: “Tonight, a Brazilian judge blocked WhatsApp for more than 100 million people who rely on it in her country.
We are working hard to get this block reversed. Until then, Facebook Messenger is still active and you can use it to communicate instead.
This is a sad day for Brazil. Until today, Brazil has been an ally in creating an open internet. Brazilians have always been among the most passionate in sharing their voice online.
I am stunned that our efforts to protect people’s data would result in such an extreme decision by a single judge to punish every person in Brazil who uses WhatsApp.
We hope the Brazilian courts quickly reverse course. If you’re Brazilian, please make your voice heard and help your government reflect the will of its people.”
Brazilian media said the order to suspend the services was related to a drug trafficking trial in Sao Paulo State.
The court tried to get access to a suspect’s WhatsApp messages but the company refused to share them, Folha newspaper reported.
The court says WhatsApp failed to comply with judicial orders in July and in August.
Judge Sandra Regina Nostre Marques finally ordered the 48-hour shut-down on December 16, after finding out that WhatsApp had persisted in ignoring its rulings.
She said the suspension order was being made under terms of Brazil’s internet legislation.
The move against WhatsApp comes as Brazilian phone companies have urged the government to restrict the use of free voice-over-internet services offered through WhatsApp.
The phone companies argue that the rise of WhatsApp has damaged their businesses.
Meanwhile other messaging services say they are benefiting from the temporary absence of WhatsApp.
One such company, Telegram, said on Twitter that more than 1.5 million Brazilian users had joined up since the court order was handed down.
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