In a statement, the Lord of the Rings director said photos shared by Bilgin Ciftci actually showed the "loveable" Smeagol.
Dr Ciftci faces imprisonment after tweeting photos of Mr Erdogan and the character in similar poses.
The court had asked experts to decide whether Gollum is good or evil.
In a statement made alongside screenwriters Fran Walsh and Philippa Boyens, Mr Jackson told the Wrap website: "We can state categorically: none of [the pictures] feature the character known as Gollum. All of them are images of the character called Smeagol."
"Smeagol is a joyful, sweet character. Smeagol does not lie, deceive, or attempt to manipulate others.
"He is not evil, conniving, or malicious - these personality traits belong to Gollum, who should never be confused with Smeagol."
Mr Ciftci's lawyer, Hicran Danisman, told the Associated Press she had been forced to argue that Gollum was not evil after a freedom of information defence failed.
Peter Jackson has waded into a court case in Turkey, which accuses a doctor of insulting President Recep Tayyip Erdogan by comparing him to Gollum.