In a surprise announcement, Karl Eller last night resigned his position as a member of the Office of the Chief Executive at the Gannett Co., citing "serious disagreement over the philosophy, policy and style of top management of Gannett."

The high-powered Eller became part of Gannett's top management team on June 6, 1979, when the company he headed, Combined Communications Corp. of Phoenix, merged into Gannett.That merger was the largest media merger in history, with Gannett paying an estimated $370 million in stock for the Arizona-based firm.

But at the time, industry analysts predicted that Eller would not remain with Gannett for very long, contending that his forceful style would contrast with that of flambouyant Gannett Chairman Allen H. Neuharth.

Besides joining a newly -- created five-man Office of the Chief Executive, Eller was also named president of Combined Communications Corp., which had become a wholly owned subsidiary of Gannett. Effectively, Eller was put in charge of Gannett's broadcast and outdoor advertising divisions. He said yesterday that he will remain in that post until the end of the year "to assure an orderly transition in management."

Two large newspapers, which had been owned by CCC -- the Oakland Tribune and the Cincinnati Enquirer -- were merged into Gannett's newspapers.

Despite predictions that there would be problems between the two men, yesterday's terse announcement was a surprise in that it was not expected so soon.

Eller said he would maintain his position on the Gannett board of directors because of his "substantial stockholding" in the firm.

In telephone calls to various Gannett directors during yesterday, Eller merely read his short resignation letter and offered no elaboration, according to some of those directors.

"It's quite a loss to the Gannett Co.," said Rollie Melton, a Gannett director who joined the company in 1977 after it purchased the Speidel chain of newspapers he headed. "He is one of the finest, strongest managers to come along in a long time."

Melton said he had no idea what drove Eller to resign.

In Rochester, Gannett Chairman Neuharth's office released the following statement:

"We accept and respect Karl Eller's decision. We wish him every success in his future personal and entrepreneurial endeavors. We have plans for the future management of Garnnett broadcast and outdoor operations which will insure their continuing success."