An American man has been arrested for defacing the Meiji Jingu Shrine in Tokyo, as Japan struggles with heavy tourist numbers and misbehaving visitors.

Tokyo Metropolitan Police allege the man used his fingernails to carve five letters into the pillar of a torii gate at the popular tourist attraction.

The five letters are believed to represent the arrested man's family names.

Police confirmed the arrest of the 65-year-old man on Wednesday, a day after the incident occurred at the sacred shrine.

Security camera footage led police to arrest him at his hotel, local news service Jiji said.

The suspect and his family arrived in Japan for sightseeing on Monday.

US Embassy staff have visited the American and are providing consular assistance, a spokesperson confirmed, although they declined to give further details due to privacy concerns.

This incident is the latest alleged example of Japan's struggle to cope with misbehaving visitors amid a boom in inbound tourism.

The case follows two incidents this year of graffiti scrawled on a pillar at Tokyo's Yasukuni Shrine, which is affiliated with Japan's wartime past.

Japan welcomed nearly 27 million visitors through September, a record pace, and their spending added 5.86 trillion yen ($37.5 billion) to the economy. 

But incidents of vandalism, public drunkenness, and "overtourism" at popular sites have sparked debate about how to handle the flood of visitors and those who flout the rules.

Flocks of tourists have forced authorities to take drastic measures to curb overcrowding and litter. In May, a small town near Mt Fuji erected a barrier to block a view of the mountain.

And in October, Tokyo's Shibuya district covered up its iconic dog statue Hachiko and enforced bans on drinking in the streets to prevent overcrowding and mischief during Halloween.

Reuters