Fifa says numerous empty seats were visible in the near-sell-out Group A match between South Korea and the Czech Republic because of fans remaining on concourses.
Football's world governing body announced an attendance of 44,985 at the 46,000-seat Estadio Akron in Guadalajara, leading to accusations they exaggerated the number of people in the stadium.
The discrepancy followed pre-tournament criticism of ticket pricing and questions over demand for a number of matches in the expanded 48-team World Cup.
"Official attendance figures reflect the number of tickets scanned and spectators present within the stadium footprint, rather than visual assessments of seating occupancy at any given moment during the match," Fifa said.
"Fifa works closely with stadium authorities and ticketing teams to ensure all published figures are based on verified operational data.
"Please note that, during last night's match in Guadalajara, several ticketed fans could be seen standing in concourses rather than staying in their assigned seats throughout the match."
The organisers also issued a picture showing a mostly full stadium.

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