He failed in an attempt to have parliament approve a public benefit test to assess the aims and activities of entities receiving tax exemptions.
On Wednesday, the Senate voted 28-6 to reject the move, his third attempt to have parliament act on the church.
Senator Xenophon told other senators that he would be relentless in pursuing a just outcome for the victims of Scientology.
Scientology had been variously accused of criminal behaviour, coercing abortions, stalking, transcending child labour laws and unconscionable treatment of members who were charged hundreds of thousands of dollars for their courses, he said.
“This is an issue that will not go away. Too many people have been hurt by this organisation.”