The church had asked Mr Justice Crockett to rule that it was a religious institution and not liable to pay State payroll tax.
The church had appealed against the refusal of the Commissioner of Payroll Tax to exempt it from paying payroll tax.
Mr Justice Crockett said an institution did not become religious in character simply because its members chose to call themselves, and the corporate body by which they were organised, a church.
He said the difficulty was that scientologists had not always so described themselves.
The predecessor to the church in Australia before 1969 was the Hubbard Association of Scientologists International, Mr Justice Crockett said.
Its aim was to promote scientology here before the Church of the New Faith was established and took over the association's activities and membership.
The judge said that despite the clerical connotation suggested by the title of the founding body in the United States, the association's title had a peculiarly secular ring about it.
"Despite the express aim of the founding church being the propagation of the religious faith known as scientology, more than once there can be found in the organisation's literature unequivocal rejection of the notion that scientology is a religion," Mr Justice Crockett said.
"There can be found in one of Mr Hubbard's publications written in the 1950's and early 1960's any claims that scientology was religious in content or intent," he said.
Mr L. Ron Hubbard was the founder of Scientology.
A board of inquiry in September, 1965, was highly critical of scientology and found that its practices were evil, the judge said.
He said the aims, objects and purpose of scientology were, he thought, accurately summed up by its principal spokesman before the Victorian Board of Inquiry when he described them as being "to increase the efficiency and well-being of the individual person, using those terms in their widest sense, and in so doing to increase the efficiency and well-being of society as a whole."
Mr Justice Crockett said: "So defined it is, I think, immediately apparent that scientology at the time that statement was made could in no sense be regarded as a religion, nor did it aspire to be so regarded.
"Indeed, the claim was expressly made that it is non-religious."
The judge said the organisations had contended that the present organisation was one that outwardly met the requirements of a religion by any definition.
He said the first "so-called Scientology Church" was the Church of Scientology of California, formed in Gevruary, 1954, of which there were 5,000 to 6,000 members in Victoria.
Mr Justice Crockett said that in 1975 the church changed its name in South Australia to Church of Scientology Incorporated.
The name change was subsequently recorded in the company's offices in New South Wales and Western Australia, where it had also been registered as a foreign company.
However, Victoria's Commissioner of Corporate Affairs has refused registration in Victoria of a like change of name.
A spokesman for the scientology organisation said yesterday that it would appeal against the Supreme Court decision.
He said scientology had been recognised legally in Western Australia 10 years ago, in South Australia, 11 years ago, and by the Federal Government seven years ago.
The decision had ignored the fact that the church was incorporated as a religion in the United States in 1954.
In NSW the church is recognised as a religious institution.