Messi played in a friendly match in Japan after missing a match in Hong Kong, which boiled over Chinese fans and sparked conspiracy theories.
The official Global Times accused Messi and his club Inter Miami of being "politically motivated" in order to "embarrass Hong Kong".
Messi has been on the bench during Sunday's game in the Special Administrative Region of China, citing injury.
He played in Tokyo on Wednesday, leading some fans to question his condition.
Messi's around 38,000 fans at the Hong Kong Stadium booed and demanded a refund when David Beckham, co-owner of Inter Miami, spoke to the table at the end of Sunday's game. Some paid as much as HK$4,880 (£494; $624) to the 36-year-old Argentine superstar.
Just last year, Messi was greeted by rock stars when he played for his national team in a friendly against Australia in Beijing. About 68,000 fans paid a whopping $680 for the chance to see him play. He is also the spokesperson for major Chinese brands such as Huawei, Chery, Tencent, Mengniu, and Chishui Wine.
Hong Kong's Secretary for Culture, Sports and Tourism, Kevin Yeung, said that he had been repeatedly told that Messi would play in the game. But with 10 minutes left in the game, they were told a hamstring adductor injury would prevent him from playing.
We immediately asked them to explore other remedies, such as Messi appearing on the pitch to interact with the fans and receive the trophy, "Unfortunately, as you can see, it didn't work out." ”
John Lee, the region's chief executive, also said he was very disappointed with Messi's absence and asked the tournament organizers for an explanation.
Hong Kong Legislative Council member Regina Ip also responded angrily, claiming that "Hong Kong people hate Messi, Inter Miami and the ** behind them" because of "deliberate and systematic snubbing".
She added: "Messi should never be allowed to return to Hong Kong. His lies and hypocrisy are disgusting. ”