Kayoko Takahashi, 53, was arrested by police in the city of Mito in Ibaraki Prefecture, about 100 kilometres northeast from Tokyo on suspicion of forcible obstruction of business.
A video filmed by her partner of 17 years, who goes by the name Hotori Amano, shows Takahashi squirting liquid from a water gun and shouting "extinguish the torch fire, I'm against the Tokyo Olympics!"
Immediately after, security personnel running with the torch bearer stop her and take her away.
According to Japanese media reports, Takahashi admitted to the allegations.
Amano, who spoke to Reuters on Tuesday (July 6), said he had no idea that his girlfriend had a water gun and had plans to disrupt the torch relay.
He also said the couple, from Hitachi, are against holding the Tokyo Olympics but came to watch the relay, as the couple enjoy festive events.