Muji joined a string of companies including hotel keeper Marriott and fashion brand Zara that Beijing has criticized this year for commercial materials that fail to reflect its territorial claims.
The government of President Xi Jinping has been increasingly assertive about its claims to self-ruled Taiwan and disputed areas of the South China Sea and East China Sea.
The national surveying administration complained a map of locations of Muji stores in a furniture catalog distributed in the southwestern city of Chongqing failed to show the Diaoyu Islands. The agency said the "problem map" contained "serious errors" in regard to Taiwan but gave no details.
The uninhabited Diaoyu islands in the East China Sea also are claimed by Japan, which calls them the Senkakus.
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In Tokyo, Japan's chief Cabinet secretary said his government has officially complained to Beijing about the order to Muji.
"There is no territorial dispute to be settled over the Senkaku Islands. We can by no means accept the measure based on China's unilateral claims," Yoshihide Suga said at a news conference, according to Kyodo News.
Zara, Delta Air Lines and medical device maker Medtronic issued apologies after being criticized by Chinese internet regulators for calling Taiwan a country on their websites.