Millions of Brazilians will not be able to access WhatsApp for two days after a judge ordered shutdown of the instant messaging mobile phone app in the country for 48 hours for failing to comply with a court order from July.

WhatsApp will be blocked in Brazil from Thursday midnight (0200 GMT Thursday), which means users of the app can access it only two days later. Brazilian phone-company association SindiTelebrasil said it received the order on Wednesday to block WhatsApp text message and Internet service for smartphones.

The WhatsApp ban order has upset many people, including Mark Zuckerberg, co-founder of Facebook, which has acquired the phone app.

"We are disappointed in the short-sighted decision to cut off access to WhatsApp, a communication tool so many Brazilians have come to depend on, and sad to see Brazil isolate itself from the rest of the world," wrote Jan Koum, CEO, WhatsApp. 

"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," wrote Mark Zuckerberg on his Facebook page. 

"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," he added.

Zuckerberg also expressed hope that the court order would be reversed, and urged the public to "make your voice heard and help your government reflect the will of its people".

Judge Sandra Regina Nostre Marques ordered the 48-hour shutdown on Wednesday after finding its continued non-compliance with a court order in a criminal case.

Band News TV network reported that the case involves a drug trafficker who has links to one of Sao Paulo's most dangerous criminal gangs, the First Command of the Capital (PCC), according to Reuters. The trafficker allegedly used WhatsApp services in carrying out crimes.