Judge Aare Kaldma of the Tartu County Court had within the space of one year been cited for fishing without a license and directing foul language at officials.
Kaldma himself had effectively petitioned the Supreme Court for his resignation, the decision signed by Ilves indicated.
Kaldma was reprimanded by the Supreme Court's disciplinary arm for the fishing violation in December 2009.
Last June, he received a 15 percent cut in pay for haranguing a telephone operator with the State Legal Assistance Information System and using the word kurat (damn or devil) on two occasions. He had reportedly had a history of such behavior.