Primary Industries, Parks, Water and Environment Department secretary John Whittington has accepted a job as the inaugural chief executive of the Blue Economy Cooperative Research Centre, which operates out of the Australian Maritime College at Newnham.

The Blue Economy CRC is an ambitious research project which brings national and international expertise under one umbrella with the aim of achieving major breakthroughs in marine renewable energy output and seafood production.

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Dr Whittington's appointment comes more than a year after reports emerged of his relationship with then primary industries minister Sarah Courtney, of whose department he was in charge.

Premier Will Hodgman made the shock announcement to Parliament in October last year, telling the house that Ms Courtney would no longer be acting as the minister after informing the premier of the relationship.

Both Ms Courtney and Dr Whittington were cleared of any wrongdoing following an Integrity Commission investigation in March.

On Wednesday, Mr Hodgman said Dr Whittington was "well placed" to lead the Blue Economy CRC.

"I take this opportunity to thank Dr Whittington for his leadership and service, in particular, the sustainable growth and management of the state's agri-food sector," he said.

"Our primary industries have gone from strength to strength, with improved environmental, biosecurity and resource management initiatives to support this growth, driven by Dr Whittington and his team.

"On behalf of the Tasmanian government, I thank Dr Whittington for his contribution and wish him all the very best in his new role."

In an email to DPIPWE staff, obtained by The Examiner, Dr Whittington told his colleagues that it had been a "great pleasure" working with them.

"Over the years we have collectively achieved much to be proud of - from big high profile projects and responses to the vitally important day to day work that we do," he wrote.

"I would like to thank each and every one for your support, effort and commitment to the Agency."

A process will be undertaken to appoint a new department secretary. DPIPWE deputy secretary Jason Jacobi will serve as the interim acting secretary in the meantime.