FBI Director Robert S. Mueller III has formally admonished the bureau official who oversees internal discipline for poor judgment in the treatment of an outspoken whistle-blower, according to documents released yesterday.

Robert Jordan, who heads the FBI's Office of Professional Responsibility, also will lose a salary bonus and will be required to take part in counseling, Mueller acknowledged in a letter to Sen. Charles E. Grassley (R-Iowa).

The punishments are the latest step in a months-long battle over the case between Mueller and Grassley, who has been sharply critical of what he calls a clubby atmosphere in the senior ranks of the FBI that has served to insulate top employees from discipline.

The flap centered on John E. Roberts, a unit chief who leads employee misconduct investigations under Jordan. Roberts told Congress last year that his career had been damaged after he helped uncover flaws in the FBI's handling of the deadly 1992 siege at Ruby Ridge, Idaho.

But when Roberts repeated similar criticisms in an October television interview, Jordan allegedly humiliated Roberts during a staff meeting and picked someone else to serve as an acting assistant in the department.

The Justice Department's inspector general, Glenn A. Fine, determined that Jordan did not intentionally retaliate against Roberts, but said he exhibited poor judgment and had left "the clear appearance of retaliation" in his actions, according to a memo he wrote that was released by Grassley yesterday. Mueller followed Fine's recommendations in meting out punishment for the incidents.

"Mr. Jordan has accepted these measures, and has expressed his intent to learn from his experience and to demonstrate that the events. . . . were isolated incidents," Mueller wrote in a letter to Grassley on Thursday.

Grassley said in a statement that "while this is a positive step, I still expect to see answers from the director as to why Mr. Jordan should remain in his current position.

"I hope in the future we learn that this case is the exception and not the rule at the FBI," he said.

Such a rebuke is rare for a senior executive at the FBI, which has been widely criticized for treating top officials with more leniency than mid- and low-level employees. Mueller, who became director amid promises of reform, has promised lawmakers that retaliation against whistle-blowers will not be tolerated.