Mr Clarke said there were many challenges ahead for the healthcare system.
"With my background in law, social services and health I'm looking forward to leading change across the primary care sector," he said in an earlier statement.
"Addressing health inequalities across Northland will be a priority, we must meet the health needs of our entire community. We need to get this right and work together to improve the health status of everyone."
Mr Clarke was a police inspector until 2008.
He entered the health sector as a senior executive in Disability Support Services at Auckland-based Taikura Trust. In 2011 he became executive director of Maori Health at Southern DHB where he helped transform health services to high-needs populations, including Maori.
During this period he completed an MBA at Otago University.
Most recently, he was chief adviser, Maori, with the Families Commission in Wellington.
Mr Clarke holds directorships on Te Putahitanga o Te Waipounamu, Whnau Ora Commissioning Agency and Te Rau Matatini, National Maori Mental Health and Addictions Workforce where he is Audit and Risk Committee chairman.
Manaia Health Primary Health Organisation (PHO) chairman Andrew Miller said the organisation underwent a rigorous recruitment process to replace Mr Farrelly who had been with the PHO for 13 years.
Dr Miller said staff had since done "an awesome job", led by acting chief executive Mary Carthew.
