Between April of 2014 and September of last year, former pitcher Shoki Kasahara, 25, is alleged to have placed wagers on 15 NPB and high school games.
Police also apprehended Satoshi Saito, 38, a former restaurant manager, on suspicion of operating a bookmaking operation for profit.
Kasahara, whose wagers were brokered by Saito, admits to the allegations.
The arrest is the latest development in a gambling probe involving four pitchers that began last year.
In November, NPB suspended Kasahara for an indefinite period after evidence of his gambling emerged. The month before, Satoshi Fukuda and Ryuya Matsumoto, were released and suspended for placing wagers on games, while a fourth pitcher, Kyosuke Takagi, received a one-year ban by NPB in March.
Both men were arrested after arriving at Haneda Airport. Police also searched six locations, including the residences of the suspects, in search of evidence connected to the case.