Aside from closing down the website, the Shanghai Cyberspace Administration said in statement that it was shutting the Marriott's mobile phone application, in a move that would also disrupt bookings.
Taiwan, Tibet, Macau and Hong Kong were on the site as being individual countries in a survey the company sent to its customers.
Taiwan, which calls itself the Republic of China, and goes under various names in worldwide organizations, has been self-ruled since 1949 in defiance of the Communist regime in the PRC.
A senior executive from one of the companies involved in the row, who asked not to be named or his employer identified, told the South China Morning Post that the issue was "serious" and that the crisis management cost, in both financial and human resources terms, would be "huge". The warnings signal that the country may deploy more sticks against foreign companies that can't risk losing business in the world's second-biggest economy.
Officials said Marriott had "seriously violated national laws and hurt the feelings of the Chinese people".
The company's Chinese language website and app has been taken offline for a week as changes are made.
Marriott, which has 124 hotels in China has apologised twice on its Weibo social media account amid calls by netizens to boycott the hotel chain. "We recognize the severity of the situation and sincerely apologize", Sorenson said in a statement.
Hong Kong and Macau, which were once British and Portuguese colonies, respectively, were handed over to the Chinese government in the late 1990s, becoming special administrative regions with certain degrees of autonomy.
Marriott reportedly promised to cooperate with the authorities for the investigation. They also suspended the Chinese app of the hotel group for one week in penance.