Also in 1998, following the resignation of Ron Davies, he was made Secretary of State for Wales, and later on First Secretary (the title would be updated to First Minister in October 2000) and leader of the Labour Party in the National Assembly for Wales. While he was the favoured candidate of the Westminster government for this role, he was less popular within Wales, and resigned in favour of Rhodri Morgan after opposition parties forced a vote of "no confidence" over the availability of Objective 1 funding from the European Union.
In 2001, he was appointed Minister of State for Rural Affairs and Local Environmental Quality, a post within DEFRA. He was the minister most closely connected with a ban on hunting with dogs, for which he attracted much criticism from hunt supporters. Michael was also criticised for the way he cited scientific research in Parliamentary debates, after citing the research of Sir Patrick Bateson as "incontrovertible" proof of need for a total ban, Sir Patrick replied, "Only somebody who was scientifically illiterate could argue that evidence from a new area of research was 'incontrovertible'" but Michael hit back saying that Bateson had misunderstood the way his work had been cited.

In 2004, he presided over the enactment of the Hunting Act which banned hare-coursing, beagling, fox hunting, mink and stag hunting in the UK from February 2005. At the time this law was being debated, and immediately after it was passed, Michael maintained his visits to rural areas despite threats and protest, but withdrew from the event to launch the "Right to Roam" stating that access to the countryside was too important to be interrupted by pro-hunt protestors whose plans could put the public at risk. Michael maintained that hunting was a "peripheral issue" citing social and economic issues in rural areas as "the day job". In 2004, he formally approved the order designating the New Forest as a National Park.
Michael retained his seat in the 2005 general election, and was moved to a ministerial post in the Department of Trade and Industry as Minister of State for Industry and the Regions. He lost his ministerial position in the Cabinet reshuffle in May 2006 and has thus returned to the backbenches.
Michael's former assistant, Lorraine Barrett, is the Welsh Assembly member for Cardiff South and Penarth.
Michael is a supporter of Somaliland and advocates for its diplomatic recognition.
Michael married in 1966 Mary Sophia Crawley, who was also at Keele University. They had five children.