Matthew Perry's former assistant Kenneth Iwamasa allegedly cleaned up more than just a house after the actor died ... prosecutors say he also tried wiping away the evidence trail tied to the ketamine conspiracy.

According to a new court filing, obtained by TMZ, federal prosecutors claim the former live-in assistant went into damage-control mode immediately after the "Friends" star's death -- allegedly directing another person to destroy ketamine evidence, shredding documents, and scrubbing digital records.

The feds say Iwamasa repeatedly lied to investigators, too ... first by allegedly hiding the fact he injected Perry with multiple ketamine shots on the day of his death, then later claiming Perry had hidden ketamine bottles himself.

Prosecutors say that wasn't true.

In the filing, they say Iwamasa instructed a person identified as "B.M." to dispose of ketamine vials and syringes after Perry died. They also allege he ordered the shredding of a ketamine prescription document and a handwritten note identifying Dr. Salvador Plasencia as a ketamine source.

The feds also say Iwamasa later admitted to some of the cleanup in a phone call with middleman Erik Fleming ... allegedly saying he "cleaned up the scene," got rid of bottles and syringes, "deleted everything," and even changed passwords on Perry's devices.

Prosecutors are pushing back hard on Iwamasa's argument that he was simply an assistant following Perry's instructions ... saying he abused the trust placed in him by both Perry and the actor's family, who believed he was supposed to help protect Perry during his addiction struggles.

Back in 2024, Kenneth pleaded guilty to one count of conspiracy to distribute ketamine resulting in death ... cutting a plea deal with federal prosecutors.