The male macaque had been terrorising the people of Hyuga in the far south of the country since late last month, and was blamed for 18 attacks.
"There are many local residents who have been bitten and injured," an official told AFP on Wednesday. "It was a serious problem for our city."
The city organised a team of 280 people on Monday to go after the creature, which was finally tracked down to an abandoned house.
Monday's hunt was the city's second large-scale attempt to capture the critter after 500 police officers, firefighters and volunteers spent a fruitless few hours looking for it on Sunday.
City officials are continuing to patrol local streets in case any more monkeys go ape, the official said.
Macaque monkeys are common in the wild throughout Japan, living on the country's heavily wooded hillsides.
