Finance Department deputy secretary David Fredericks will join the public service's top brass after he was appointed secretary of the Environment and Energy Department.

Treasury deputy secretary Simon Atkinson will lead the Department of Infrastructure, Transport, Cities and Regional Development.

He replaces Steven Kennedy, who left the department to become the Treasury secretary.

Mr Fredericks takes on his new job after former Environment and Energy Department boss Finn Pratt announced in October he would retire.

The new departmental leader was deputy secretary in the Attorney-General's Department from 2011 to 2015 and a ministerial adviser from 2008 to 2010.

Before that he served in the Solomon Islands' Ministry of Treasury and Finance.

Mr Atkinson has had senior roles in the Infrastructure and Regional portfolios and led the establishment of Infrastructure Australia.

He has also worked in the departments of Defence and Finance, served as cabinet secretary from 2017 to 2018, and was a ministerial adviser from 2013 to 2016.

Both Mr Fredericks and Mr Atkinson have been appointed for five years and start on November 11.

The bureaucracy's senior leadership has had several changes this year, including Martin Parkinson's departure from the Prime Minister's Department and his replacement by former Treasury boss Phil Gaetjens.

Mr Morrison announced in September he would re-appoint Mike Pezzullo as Home Affairs Department secretary and Chris Moraitis would continue as Attorney-General's Department boss.