An agency spokesman acknowledged the banner, put up in front of the agency's headquarters in March to celebrate its 10-year anniversary, had the horizontal stripes in descending order as white-red-blue instead of the Russian flag's white-blue-red, RIA Novosti reported Monday.
"The mistake was caused by the wind, which turned the banner upside down," the spokesman said.
However, turning the Russian flag upside down would make it red-blue-white, not white-red-blue, RIA Novosti said.
The banner, which was the subject of online criticism, was taken down Monday.
News website Pravdevglaza.ru said anonymous sources inside the agency reported the mistake was reported to officials months ago, but bosses did not want to spend the money for a replacement. The news website said officials dubbed the white-red-blue flag "the flag of the Galaxy" to distinguish it from the Russian flag.