After the election of 1998 Remkes was appointed as State Secretary for Housing, Spatial Planning and the Environment under the Second Kok cabinet taking office on 3 August 1998.

Remkes continued to be active in politics and in June 2010 was nominated as the next King's Commissioner of North Holland serving from 1 July 2010 until 1 January 2019.

Remkes also became active in the public sector as non-profit director and serves on several state commissions and councils on behalf of the government.

After the election of 1998 Remkes was appointed as State Secretary for Housing, Spatial Planning and the Environment in the Cabinet Kok II taking office on 3 August 1998.

The Cabinet Kok II resigned on 16 April 2002 following the conclusions of the NIOD report into the Srebrenica massacre during the Bosnian War and continued to serve in a demissionary capacity.

On 29 June 2006 the Democrats 66 retracted their support for the cabinet Balkenende II after criticizing the way Minister for Integration and Immigration Rita Verdonk (VVD) had handled the crisis around the naturalization of her party fellow elected to the House of Representatives Ayaan Hirsi Ali.

Remkes remained in active politics, in June 2010 he was nominated as the next Kings's Commissioner of North Holland serving from 1 July 2010 until 1 January 2019.