Screenshots of an internal email purportedly sent to Emirates staff circulated online this week, telling cabin crew to use the Chinese flag instead of Taiwanese flag pins. The directive was linked to a demand from the Chinese government, the email said.
China regards Taiwan as a renegade province after defeated Nationalists fled there in 1949, after losing a civil war to the Communists. Beijing has not ruled out the use of force to bring the self-governed island under its control.
Taiwan's foreign ministry told Reuters its representative office in Dubai had protested to Emirates.
"A few hours later the company e-mailed to apologize, and said the request was not correct and was not appropriate, but that it still asked Taiwanese crew members to not wear any flag badge, including our flag," the ministry said in a statement.
Emirates is not ordering its Taiwanese crew to wear China's flag badge, the ministry said.
Emirates did not comment directly on the screenshots, but said that an internal email on Tuesday told cabin crew to remove a flag pin from their uniforms and replace it with another.
"This email was sent in error and has since been retracted. Our intent is to recall the flag pins worn by all our cabin crew as part of our uniform update," an Emirates spokeswoman said.
Chinese Foreign Ministry spokesman Hua Chunying told a daily briefing she had not heard of the incident and did not know anything about it.
Relations between the two sides have cooled since Taiwan President Tsai Ing-wen took power last year, because she refuses to concede the self-ruled island is part of China, and Beijing fears she wants to push it toward formal independence.
"Recently, China has repeatedly pressured us on political factors, harming the rights of our nationals. This is very improper and the wrong behaviour. We cannot accept this," the island's China policymaker, the Mainland Affairs Council, said in a statement when asked about the matter by Reuters.
Emirates flies to five cities, including Beijing and Zhengzhou in mainland China, which is set to overtake the United States as the world's largest aviation market by 2024. It flies daily from Dubai to Taipei.
Hundreds of Internet users left images of the Taiwanese flag and comments on Emirates Facebook page on Wednesday, criticising the internal email.
"Even if the one-China policy is to be respected, they should have tried discussing this problem and finding an alternative solution with their Taiwanese employees before issuing such a letter," said a user who goes by the name Barton Cheng.