Apple removed both the English-language and Chinese-language apps from the iTunes store in China on Dec. 23, according to the New York Times, which first reported the action.
"The request by the Chinese authorities to remove our apps is part of their wider attempt to prevent readers in China from accessing independent news coverage by The New York Times of that country," the New York Times spokeswoman Eileen Murphy told Reuters.
"We have asked Apple to reconsider their decision," Murphy said.
The Chinese government began blocking The Times's websites in 2012, after a series of articles on the wealth amassed by the family of Wen Jiabao, who was then prime minister, according to the New York Times report.
"We have been informed that the app is in violation of local regulations," Fred Sainz, an Apple spokesman told the Times.
However, apps from other international publications, including The Financial Times and The Wall Street Journal, were still available in the app store, the New York Times reported.