The match had been arranged as part of Mexico's tour of Europe next month on their way to South Africa with friendlies against England, Netherlands and Italy.
"(The match on) May 30 against Portugal won't go ahead, we couldn't overcome those little details which arose," Nestor de La Torre, the Mexican federation's director of national teams, said on Monday.
"The coach (Carlos Queiroz) asked me to let them have the (Thaba Ya Batswana) hotel, of course there was a no from us, so in a chat they mentioned they were not prepared to be flexible because we didn't leave the hotel to them," he told reporters.
Mexico will be based at the hotel in Johannesburg during the finals starting on June 11 with their Group A match against hosts South Africa. They also face France and Uruguay.
De La Torre said Mexico would seek an alternative opponent to play on May 30.
Coach Javier Aguirre's team have warm-ups in the United States against Ecuador, Senegal and Angola before a friendly at home to Chile in Mexico City on May 16.
