The manual was a "sacred text" and covered by copyright ownership, the court ruled.
The case was part of a legal fight between Zenon Panoussis and the Church of Scientology. In September 1998, the Stockholm District Court ruled that Panoussis had violated copyright laws when he published the manual on the Internet.
Panoussis also distributed copies to parliament and other institutions to allow non-church members access to the manual in accordance with Sweden's freedom of information act.
In its ruling, the appeals court said the scientologists had treated the material as confidential such as by requiring members to sign agreements about not revealing the details of the texts.
"We are very pleased with the ruling. It shows that the justice system works," church spokeswoman Tarja Vulto said. The case "was about copyright, and that the copyright owners have the right to their own material," she added.
Panoussis was ordered to pay trial costs of 435,000 kronor ($42,000) for the appeals court trial. This was in addition to the $150,000 he was ordered to pay by the district court.
Last May, scientology ministers were granted the right to conduct marriages in Sweden. This followed a decision in March 2000 to recognize the church as a religious community. Previously, it was considered a nonprofit organization.
The Church of Scientology was established in Sweden in 1968. It has roughly 3,500 members in Sweden, Vulto said.
Scientology is recognized as a religion in the United States, but in Europe it has struggled for acceptance.
The church, which has about 8 million members worldwide, was founded by science-fiction writer L. Ron Hubbard in 1954. Hubbard's book "Dianetics" formed the basis of his philosophy that traumatic memories in past lives could be cleared through church counseling.