More than 5,000 people with tickets skipped Uruguay's 1-0 win over Egypt in the opening game at Yekaterinburg.
FIFA says it is investigating why, with "no-shows" one of the factors.
Pockets of orange seats were clearly visible in the lower tiers of the stadium which has a 33,061 capacity for World Cup games.
FIFA says it allocated 32,278 tickets and the official attendance was 27,015 for the 5 p.m. local time kickoff.
A FIFA spokesman said: "We can confirm that the official attendance for the match between Egypt and Uruguay in Ekaterinburg is 27,015. The FIFA World Cup stadium capacity is 33,061.
"The fact that the actual attendance is lower than the number of allocated tickets can be due to different factors, including 'no shows' on match day, which FIFA is currently investigating."
Yekaterinburg is the furthest east of Russia's 11 host cities and is about 880 miles east of Moscow in the Ural Mountains, which are traditionally considered the border between Europe and Asia.
"There were some bald spots and it wasn't very pleasant," regional sports minister Leonid Rapoport told Russia's RIA Novosti state news agency.
FIFA records show the last World Cup match with a smaller crowd was Paraguay's 2-0 win over Slovakia in South Africa in 2010, which attracted 26,643 fans. Five days before that game, 23,871 attended a 1-1 draw between New Zealand and Slovakia, the smallest number recorded for any World Cup game this century.
At the last World Cup in Brazil, no game had fewer than 37,000 people in the crowd.