He will be responsible for leading the work of eight government departments in the UK's largest and wealthiest region, with 19 county and unitary authorities, and a budget of£670m.
The regional director reports to the Office of the Deputy Prime Minister, which includes responsibility for local government and the regions.
Mr Martin, joined Peterborough in 1997 as director of community services and was promoted to chief executive in 1999. He previously worked at Cambridgeshire CC for six years, and before that at Manchester City Council, Bolton MBC and Nottinghamshire CC.
He replaces David Saunders at the end of August.