The fire had raged in the mountains around the rural region since February 26, killing at least one person, damaging at least 210 buildings and forcing more than 4,200 residents to flee their homes, local officials said.
"Following an aerial survey, we assessed that the fire no longer posed the risk of further spread. I declare that the fire is now under control," Ofunato Mayor Kiyoshi Fuchigami told a news conference.
The fire engulfed about 2,900 hectares (7,170 acres) -- around half the size of Manhattan -- making it Japan's largest in more than 50 years.
It surpassed the 2,700 hectares burnt by a 1975 fire on Hokkaido island.
Wet weather that began on Wednesday following a record dry period helped firefighting efforts.
Japan endured its hottest summer on record last year as climate change pushes up temperatures worldwide.
Ofunato received just 2.5 millimetres (0.1 inch) of rainfall in February, breaking the previous record low for the month of 4.4 millimetres in 1967 and far below the average of 41 millimetres.
The number of wildfires in Japan has declined since a peak in the 1970s.
Wildfires in Japan tend to occur between February and May, when the air dries out and winds pick up. There have been around 1,300 a year in recent years.
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