Officers took Mitsuyoshi Kamiya into custody on the southern tropical island of Okinawa on Thursday, on suspicion of making three calls to the embassy mentioning bombs earlier this month, a police spokesman said.
"Bomb Camp Schwab (in Okinawa). Bomb embassy," he said in English on the phone, according to the spokesman.
Camp Schwab, a US military base on Okinawa, is the site of a planned air station relocation which will see it hosting half of the 47,000 American military personnel in Japan.
Mired in protests for years, it is the focus of much of the friction between Okinawa, Japan's poorest prefecture, and the central government in Tokyo.
Kamiya admitted making the bomb telephone calls, the police spokesman said. He has not presently been charged with threatening to kill the ambassador.
Kennedy, the last surviving child of assassinated US president John F. Kennedy, took up her post in Tokyo in November 2013 as the first woman US ambassador to Japan.
Japanese television station NTV reported Monday that Japanese police were investigating death threats made by an anonymous caller against her.
US officials said they had been co-operating with Japanese authorities on the bomb and death threat calls for some time.
"We are working and have been working for several weeks with the Japanese government on these reports, these threats," State Department spokeswoman Jen Psaki told reporters in Washington.
"The Japanese police arrested a 52-year-old individual from Okinawa for making threatening phone calls against the embassy... Not just related to the ambassador," Psaki said.
The arrest was "a positive step," she said, adding the State Department would stay in close touch with Japanese authorities.
The news of the threats came only weeks after the US ambassador to South Korea, Mark Lippert, was stabbed during a public event in Seoul.
Lippert had to have 80 stitches to his face and was hospitalised for five days after being attacked by a knife-wielding nationalist during a breakfast event in the South Korean capital.
Psaki stressed there was no connection between the attack on Lippert and the threats against Kennedy.
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