The newspaper claimed this was a potential escalation of the tech war between the US and China.
Apple told the NYT it had complied with the orders from Beijing as it had no choice but to do so, even if it disagreed.
Also removed from the app store on Friday were Dubai-based Telegram and US-based Signal, with these claims attributed by the NYT to Appfigures, a market research company.
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The US and China have been involved in a tit-for-tat trade war ever since Donald Trump initiated it back in 2018. The most recent action taken by the US was a decision to raise tariffs on imports of Chinese steel and aluminium.
The US has also been blocking sales of advanced semiconductors to China and blocked Huawei Technology, China's biggest telecommunications outfit, from participating in 5G rollouts after lobbying many of its allies to do likewise.
The US House of Representatives is preparing to vote on a bill to force Chinese firm ByteDance to choose between selling its TikTok app or else have it banned in the US.
The NYT said WhatsApp had been downloaded 15 million times in China while Threads, which was started by Facebook when Twitter, now known as X, hit some hurdles after it was bought by Elon Musk, had been downloaded 470,000 times.