Most of the affected users said they could not send or receive photos using the chat app, which is owned by Facebook, without a virtual private network.
VPNs are used to skirt Beijing's censorship system – which blocks websites with information that could be critical of the Communist Party such as YouTube, Twitter and foreign news sites – by rerouting internet traffic elsewhere.
Some users said they could not get WhatsApp to connect to the internet on Tuesday without a VPN.
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In a test conducted by the South China Morning Post in the afternoon, two users registered with mainland Chinese mobile numbers were unable to send videos or pictures to each other via WhatsApp.
One of the users then tried, and failed, to send the video and photo files to an overseas number. When that person tried to send a photo to the mainland Chinese user from overseas, the message was received but the photo was only displayed as a loading thumbnail.
There was no problem sending and receiving text messages, and all services appeared normal when connected to a VPN.
Beijing's ongoing campaign to "clean up" the internet has seen VPN providers shut down, celebrity gossip accounts closed and video content restricted.
WhatsApp is one of the few foreign messaging apps available in mainland China. WhatsApp is not as popular as the local app WeChat, but it is favoured by some for its end-to-end encryption.
WeChat, however, which is owned by tech giant Tencent, has been found to be censoring messages deemed sensitive by Beijing without notifying its users, according to reports by Toronto-based Citizen Lab.
A member of a non-governmental labour welfare group in Shenzhen, who did not wish to be named, told the Post he had been unable to use WhatsApp since 8am, but other apps on his phone, including WeChat, were fine. He regularly uses WhatsApp to communicate for work as the messages are encrypted. "WhatsApp is much safer than WeChat," he said. "Today I didn't talk to my colleagues at all. It's very confusing."
WhatsApp and Facebook did not respond to requests for comment. Facebook's flagship social networking site and its photo-sharing service Instagram are both blocked in mainland China. Foreign chat apps blocked in recent years include Tokyo-based Line and Berlin-based Telegram.