But today, Frank Keith, a spokesman for the Internal Revenue Service, said that as part of the settlement the Government had decided to classify the sprawling empire as a charitable and religious organization.

Mr. Keith said the group was notified of the decision on Oct. 1 and that it followed a two-year review of financial statements and other information provided by the organizations about their structure and purposes. He would not say whether the final decision had been made by the new Commissioner of the Internal Revenue Service, Margaret M. Richardson, who would normally have to approve any large settlement.

The ruling means that the church and more than 150 related educational and counseling groups will no longer have to pay Federal income taxes. Church members may also deduct their membership dues from their taxes. Mr. Rathbun said that the groups did not expect to receive refunds of back taxes because they had not been assessed for many of the years that they were contending to be a religious organization. Conciliatory Tone

Mr. Rathbun was unusually conciliatory toward the I.R.S. today. He said the church had prevailed after what he called "an objective review" under the auspices of John Burke, an assistant commissioner who heads the agency's Employee Plans and Exempt Organizations division.

The Church of Scientology has branches around the world and has its headquarters in Los Angeles. It calls itself a "new religion," one not based on the worship of a god, but rather one that purports to teach members how to improve the quality of their lives. Instead of salvation, it promises to rid the mind of mental obstacles to happiness and help members improve the world.

But some courts and many former members have called the organization a sham, saying it relies on religious pretenses to mask a highly profitable business. Membership in Dispute

The group claims a membership of eight million, although former members say that those figures are grossly inflated and that the total is probably closer to 50,000.