The probe which comes less than a year after Japan made the possession of child porn illegal reportedly follows the arrest of two men in September for posting illicit photo books featuring children on the Internet retailer's website.
In response to the allegations, the US-based company's Japan unit said Tuesday that it was working with police. It did not supply further details or confirm the raid.
"We take this investigation seriously and we are cooperating fully with the authorities," the firm said in a statement sent to AFP.
"We don't permit illegal items on our site, and we have systems and processes designed to prevent and remove illegal items from being listed.
"We are committed to enforcing our policies and the law for items listed on our site," it added.
Japanese media said police searched the head office of Amazon Japan K.K. and a distribution centre in Chiba outside the capital on Friday.
The Sankei newspaper has also reported police discovered that about 10 arrested child-porn vendors had earlier put up nude photo books and other material on Amazon Japan's website.
"We couldn't get child porn merchandise up on other major shopping sites but we could on Amazon," the daily quoted one of the vendors as telling police.
Authorities did not immediately comment on the reported raid or other details.
Japan has a large porn industry, and visitors are sometimes shocked by the ubiquity of sexual imagery and the huge volume of material available.
In June, Japan fell into line with other major developed countries and banned the possession of child pornography, but the sometimes graphic paedophilic images in manga comic books remained legal.
Campaigners had long urged Japan to toughen its stance on child pornography, complaining it was a major source of the material for global markets.
The new legislation banned possession of photographs and videos depicting real children aged below 18, but it does not include drawings or digitally-created imagery.