Akitoshi Okamoto is accused of making thousands of calls to KDDI's free number in just eight days, accusing them of violating his contract.
The company told local media he had been calling repeatedly for a total period of two-and-a-half years.
Mr Okamoto denies harassing the firm, and told the police he was the victim in the situation.
Japanese media report Mr Okamoto accused KDDI of violating his contract because his phone was unable to pick up radio broadcasts.
Tokyo's Metropolitan Police said that when Mr Okamoto called the company, he would either insult its customer service staff or demand that a representative visit him to apologise.
Sometimes, a spokesman added, he would call the company's customer service line only to immediately hang up.
KDDI said it initially hadn't wanted to press charges, but his calls became so frequent and relentless that it was unable to deal with other customers.
A police spokesman told AFP news agency that Mr Okamoto was arrested on suspicion of "fraudulent obstruction of business" - a charge that can be brought against people in Japan who make it impossible for a business to run normally.