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WASHINGTON — The Environmental Protection Agency’s internal watchdog has rebuked the agency’s chief of staff for refusing to cooperate with an inquiry into whether he pressured a scientist to alter her congressional testimony, calling his actions a “flagrant problem” and referring the matter to Congress.

In a letter made public on Wednesday, the E.P.A.’s acting inspector general, Charles J. Sheehan, told the agency’s administrator, Andrew Wheeler, that his chief of staff, Ryan Jackson, was in “open defiance” of two separate inquiries, an audit and an investigation, though details of the second matter remain unknown.

“To countenance open defiance even in one instance — much less two, both by a senior public official setting precedent for himself and all agency staff — is ruinous,” Mr. Sheehan wrote.

An E.P.A. spokesman said Wednesday that Mr. Wheeler had directed Mr. Jackson to sit down with Mr. Sheehan’s office for an interview.