Argentina were scheduled to play Nigeria in the Chinese city of Hangzhou next month before facing the Ivory Coast in Beijing, but Messi's failure to take the field for Inter Miami in Hong Kong on Sunday caused widespread anger among fans.
The organiser of the Hong Kong match said they would give fans a 50% refund for tickets after the Argentine did not take the field due to injury, but played in Japan days later.
The backlash grew on Friday, with Hangzhou sports authorities saying that Argentina's friendly against Nigeria would no longer take place.
"As a commercial event, a company and the Argentinean soccer team negotiated that the team would play a friendly match in March this year in the city of Hangzhou," the Hangzhou authorities said in a statement.
"In view of the current well-known reasons, according to the competent authorities, conditions to hold the friendly match are not mature, therefore (we) have decided to cancel it."
It was not immediately clear if Argentina's other friendly against Ivory Coast in Beijing would also be cancelled.
The Chinese FA did not immediately respond to an emailed request for comment sent outside normal business hours. The Argentine FA also did not immediately respond to an emailed request for comment.
Tatler Asia, a privately owned publishing and lifestyle company, said in a statement on its Instagram page that it was "deeply sorry" and "heartbroken" that fans were let down after Messi stayed on the bench during Sunday's match.
TICKET REFUNDS
The match in Hong Kong drew 40,000 fans, with some spectators paying up to nearly HK$5,000 ($640) per ticket.
The cost of all match tickets bought from official channels can be 50% refunded, Tatler said, adding that it had been in discussions with the Hong Kong government to resolve the issue.
Inter Miami head coach Gerardo "Tata" Martino said Messi was deemed unfit to play in the friendly in Hong Kong, but he came on as a 60th-minute substitute against Vissel Kobe on Wednesday.
"When we learned that Messi would not be playing, we pleaded with Inter Miami CF ownership and management to urge him to stand up, engage with the spectators and explain why he couldn't play," Tatler said.
"He didn't. The fact that Messi and (team-mate Luis) Suarez played in Japan on February 7 feels like another slap in the face."
In the match in Tokyo, entire blocks of seats at the Japan National Stadium were unoccupied, with just 28,614 tickets sold.
Chinese state media, Hong Kong politicians and some fans swiftly condemned Messi's participation in the Japan match, with state-controlled Global Times writing that his absence posed many questions on the differential treatment for Hong Kong.
In a statement, Hong Kong's government said Tatler Asia had made its best efforts to arrange a refund, adding that many people had questions about the incident.
"The government hopes that the Inter Miami team will eventually provide a reasonable explanation to Hong Kong citizens and fans who came to Hong Kong to watch the game."
Tatler Asia said Inter Miami had committed to ensuring that their top players, including Messi and Uruguay's Suarez, would play for 45 minutes unless injured.
It said it had hoped to create an iconic moment in support of the government's efforts to remind the world how relevant and exciting Hong Kong is.
"That dream is broken today for us and all those who bought tickets to see Messi on the pitch."