On 10 May 1940 Nazi Germany invaded the Netherlands and the government fled to London to escape the German occupation.

The Cabinet De Geer II fell on 26 August 1940 after a conflict between Queen Wilhelmina and Prime Minister Dirk Jan de Geer and continued to serve in a demissionary capacity until it was replaced by the Cabinet Gerbrandy I with Van Rhijn continuing as Minister of Agriculture and Fisheries, taking office on 3 September 1940.

Van Rhijn was appointed as State Secretary for Social Affairs in the Cabinet Drees–Van Schaik, taking office on 15 February 1950.

After the election of 1952 Van Rhijn again continued as State Secretary for Social Affairs and Health in the Cabinet Drees II, taking office on 2 September 1952.

He holds the distinction as the second longest-serving State Secretary for Social Affairs after Louw de Graaf with 8 years.