Bougainville's chief secretary, Joseph Nobetau, has been sacked but he says the government does not have the constitutional power to fire him.
The president of the autonomous Papua New Guinea region, John Momis, announced on Saturday that Mr Nobetau had been removed from his office.
He said the relationship between the government and Mr Nobetau had been strained for some time, with matters coming to a head when he was accused of incompetence and insubordination.
Mr Nobetau was cleared of those allegations but Mr Momis said the relationship had become untenable.
Over the past year Mr Nobetau had been leading a vigorous campaign to rid the Bougainville public service of corruption, with dozens of people being convicted or losing their jobs.
He had been following up an audit done by the PNG Departments of Personnel Management and Finances.
This showed Bougainvillean public servants had been stealing by claiming allowances they were not entitled to, were being paid salaries well in excess of their classification level and were paying themselves while not turning up for work.
Mr Nobetau said under the constitution, senior public servants could not be removed by the government, as a means of protecting the independence of the public service.
He said he was now considering his options.