The Japan Fair Trade Commission (JFTC) accuses Google of breaking the law by imposing "transactions with binding conditions" on Android smartphone manufacturers in Japan.
Specifically, it says Google made sure that its online app store Google Play needed to be installed as part of a package with its web-browser search app Chrome.
Google Play is so widely used that without it, "Android devices are basically unsellable", the source told AFP.
The JFTC also believes Google dangled financial incentives to pressure these smartphone makers into excluding rival search apps, said the source, who declined to be identified because the information is not yet public.
Such behaviour constitutes "unfair trading practices" banned by the antitrust law, the source said, adding that a cease-and-desist letter would be sent to Google pending a hearing.
Such administrative action is a "fairly strong" measure taken by the JFTC, the source said, and the first against the GAFAM -- an abbreviation for US tech behemoths Google, Amazon, Facebook, Apple and Microsoft.
Google Japan was not immediately available for comment when contacted by AFP.
The move mirrors similar crackdowns on Google in the United States and Europe.
The US government asked a judge in November to order the dismantling of Google by selling its widely used Chrome browser in a major antitrust crackdown on the company.
Meanwhile the European Commission, the EU's executive, recommended last year that Google should sell parts of its business and could face a fine of up to 10 percent of its global revenue if it fails to comply.
In Japan, the JFTC is playing hardball with other US tech giants that it sees as behaving in an anti-competitive manner.
Last month, the agency conducted an on-site inspection of Amazon's Japanese subsidiary in Tokyo, accusing it of abusing its industry dominance to drive down prices.
Amazon Japan used its coveted "buy box" -- a prominent spot on its website -- against sellers, pressuring them into lowering prices to give it a competitive edge over rival e-commerce sites, the JFTC said.