Three high-ranking Interior Department officials will be leaving by the end of the month, including the head of the agency's controversial mineral-leasing programs, administration sources confirmed yesterday.

According to the sources, Interior Secretary William P. Clark told his staff yesterday that assistant secretaries Garrey E. Carruthers, G. Ray Arnett and Kenneth L. Smith would resign.

Carruthers is in charge of the department's energy and minerals office; Arnett runs the fish, wildlife and parks programs, and Smith oversees Indian affairs.

While rumors had been widely traded in recent months that shakeups were imminent at Interior, environmentalists were stunned yesterday at the abruptness of the resignations, all of which are expected to take effect before Nov. 30.

Interior officials said that the personnel moves do not presage changes in department policy and that all three men had decided on their own to pursue other career opportunities.

But outside the agency, the departures were widely interpreted as a sign that Clark intends to continue a steady move away from the confrontational policies of his predecessor, James G. Watt.

"This is a symbol, I think, that . . . is reflective of Clark changing the Interior Department from the Watt stamp to the Clark stamp," said Paul J. Pritchard, president of the National Parks and Conservation Association.

Arnett, in particular, had earned the enmity of many conservation groups, who considered him inflexible and combative. Arnett survived a shakeup shortly after Clark took over last year, however, and many in the conservation community believed that he would remain through President Reagan's next term.

"He was not a favorite of ours," Pritchard said. "He is a gentleman, and he certainly has the ear of the president. But he was not sympathetic to the parks, and he was so unsympathetic that it seemed he didn't care about them."

The most significant vacancy created by the resignations is the job held by Carruthers, who last year assumed control of virtually all of the department's mineral leasing programs as well as its surface-mining office and the 350 million-acre domain of the Bureau of Land Management.

While congressional moratoriums are likely to keep the pace of offshore development well under the breakneck speed envisioned by Watt, a similar moratorium on coal sales was lifted this year.

Carruthers is expected to return to New Mexico State University, where he holds a tenured position, and is understood to be considering a bid for governor. Arnett reportedly is in the running to head the National Rifle Association.

Smith, a member of the Wasco tribe of Oregon, also has taken political heat in the past four years. Tribal organizations considered him an administration apologist who failed to protect programs from budget cuts at a time when other agencies were counting on Interior to pick up the slack when their Indian programs were cut.

But he also had his defenders, who generally said Smith was asked to shoulder an impossible task.