The man turned out to be a military police officer who had been sent to the restricted area at Sao Paulo's Corinthians Arena unbeknownst to the civilian police, and no shot was fired, authorities said.
President Dilma Rousseff and a dozen of world leaders were on hand for the opening ceremony and Brazil's 3-1 victory over Croatia, along with more than 60,000 fans.
"A civilian police sniper detected the presence of someone carrying a gun and wearing a bulletproof military police vest in a restricted area," Sports Minister Aldo Rebelo told a press conference.
Authorities denied the request while they checked the man's identity, the minister said. Once identified, he was removed from the area.
The public security secretariat for Sao Paulo state sought to downplay the incident, which it called "a communication error" that was quickly corrected.
"At no point was the security of the authorities or the fans put at risk," it said in a statement.
It said there was a three-part protocol for a police sniper to open fire: he must receive permission to load his rifle, which is kept unloaded for security reasons; receive permission to take aim; and receive permission to shoot.
Brazil's civilian police are mainly an investigative force, while the military police are charged with public security though some units have taken on different roles during the World Cup.
The sniper involved in the incident was from the civilian police's special rescue unit.
Newspaper Folha de Sao Paulo said the military policeman involved was from a tactical unit and was in the area investigating a bomb alert that turned out to be a false alarm.
The sniper, who was not informed of the military policeman's presence, feared he was an attacker disguised in police uniform, said the daily.
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