A report in the Wall Street Journal on Wednesday noted that the withdrawal of both the English and Chinese language apps further curtails access to the Times in China.
Since its publication in 2012 of a report detailing the wealth of China's top leadership and their families, New York Times Co.'s website stands blocked in China.
"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 which is no different from the journalism we do in every other country in the world, including the US," said Eileen Murphy, spokesperson of the Times, while asking Apple to reconsider its decision.
The Times app is not permitted to display to China users "for some time" because Apple was informed the app was in violation of local regulations, said Apple Spokesman Fred Sainz.
Franz did not comment on the regulations but said Apple would make the app available in its store when "this situation changes".
China is known for banning digital sites like Facebook and Google that it believes harms its national security or promote misinformation. The Wall Street Journal's Chinese-language site has been blocked since 2014.
In 2013, China listed Apple among the websites and app stores that were being investigated for promoting pornographic content. However, the findings of the investigation are not known.