Patricia Espinosa, the Mexican foreign minister, accused China of discrimination after Beijing ordered dozens of Mexicans into quarantine across the country, although only one, a man now in Hong Kong, was found to have the H1N1 flu.
China has denied the charge, saying isolation was the correct procedure.
According to the Chinese health ministry, none of those quarantined had shown any signs of being infected.
The state-run Xinhua news agency said the Mexicans in Beijing were doing well inside a hotel where they have been confined, though the air conditioning has been turned off to prevent any spread of disease despite temperatures reaching 30 degrees Celsius outside.
Meanwhile, many of the Chinese tourists in Mexico said they were glad to be leaving, citing concerns about the H1N1 virus.
"I just finished my holiday and a friend told me something terrible was happening in Mexico and now I just want to go home to my country," Li Dong Mei, a tourist, told Reuters news agency.
"We were a bit worried because of the influenza and because of the situation. The government sent us a plane and now we are able to go home so it's very good," Bao Mao, another Chinese tourist, said.
Mexico has been at the centre of the flu outbreak, prompting the authorities to order a five-day nationwide shutdown in an attempt to contain the influenza.
Countries across the globe have also reported similar cases and on Monday, the World Health Organisation (WHO) said more than 1,000 confirmed cases of the flu had been reported from about 20 countries.