Making the announcement, Prime Minister John Key said Mr Hughes had dedicated his working life to the public service.
"The State Services Commissioner is a vital role, leading and overseeing the performance and integrity of the State Services, employing most public service chief executives, as well as driving the ongoing improvements of the State sector and how it operates.
"Peter has strong relationships with other public service leaders, Ministers and Members of Parliament across the political spectrum, as well as business, industry and union leaders. He will be an effective leader of our public service."
The State Services Commissioner is appointed under the State Sector Act 1988 by the Governor-General on the recommendation of the Prime Minister.
The Minister of State Services had oversight of the recruitment process on the Prime Minister's behalf.
Mr Hughes, who holds a Master's Degree in Public Administration from Harvard University, has served as deputy Director-General of Health, chief executive of the Health Funding Authority and secretary for Internal Affairs.
In 2001 he was appointed chief executive of the Ministry of Social Development, a role he held for 10 years before becoming Professor of Public Management and head of the School of Government at Victoria University of Wellington from 2011 to 2013.
During his time in the role, Mr Rennie, who was paid $650,000-$659,000 last year, introduced disclosure requirements for chief executives of Government departments and agencies, including travel expenses and gifts.
Mr Rennie also oversaw the current Government's restructure of the core public service, including a cap on the number of bureaucrats.
He was at the centre of controversy in 2014 for his part in a press conference with former Cera boss Roger Sutton over allegations of inappropriate conduct towards staff. Mr Sutton announced he was stepping down at that press conference but also gave details of his actions, despite an agreement not to talk about the complaint.
Labour leader Andrew Little called for Mr Rennie to be stood down for his part in the press conference and Mr Rennie later expressed regret for allowing it to take place.