Facebook-owned WhatsApp and Telegram are popular messaging apps among smartphone-using Afghans -- including Taliban and Islamic State jihadists.
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So far state-owned Salaam Network is the only internet provider to obey the order, which applies from November 1 to November 20, telecommunications ministry spokesman Najib Nangyalay told AFP.
"We are testing a new technology and WhatsApp and Telegram will be temporarily blocked," Nangyalay said.
"It is not a blow to the freedom of communication in Afghanistan -- we have access to Facebook, Twitter. We are committed to the freedom of expression."
Acting telecommunications minister Shahzad Aryobee said the move was in response to dissatisfaction with the services -- something industry insiders rejected.
"In order to improve the services and solve the technical problems of these two programmes the Ministry of Telecommunication and Information Technology is considering to introduce a new technology," Aryobee said in a Facebook post on Friday.
Testing is "time-consuming" and required the temporary stoppage of WhatsApp and Telegram.
The move has ignited a firestorm on social media with users describing the move to block the messaging services as an assault on their right to free speech.
"Blocking WhatsApp and Telegram is the beginning of censorship by the Afghan government and bringing the virtual world under their control in Afghanistan. I think this is intolerable," Facebook user Abdullah wrote.
Another user Mahdi Yasir said the quality of WhatsApp and Telegram "are great" and urged the government to focus on closing "factories producing Pakistani suicide bombers" instead.
"The two applications we were using the most are blocked. God damn this government," Abdulraouf Sharifi posted.
A telecommunications official scoffed at the government's claim to be developing a new technology.
"They are not going to match an international standard app," he said.
"WhatsApp is very popular because it uses less data and the quality is very good.
"It could be security related (but) if they block it people can access VPNs," he added, referring to virtual private networks.
Around eight million people, largely in Afghanistan's major cities, can access the internet, up from almost none during the Taliban's repressive 1996-2001 regime. Most do so through mobile phones.
The Taliban frequently uses WhatsApp to post statements in Afghanistan while IS militants favour Telegram.
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