He took part in Croatia's first post-independence parliamentary elections in 1992 and was elected as a member of the Croatian Democratic Union. From 12 August 1992, to 12 October 1993, he served as Croatia's Minister of Health.[4] He served as a minister without portfolio from 12 October 1993, to 7 November 1995, won reelection in 1995, and served again without portfolio from 13 November 1996, to 19 December 1997.[5][6] From 19 December 1997, to 27 January 2000, he served as Minister of Defenders from the Homeland War.[6] He was reelected again in 2000 and retired in 2003.[7]
Njavro wrote a book about his internment during the war entitled Glava dolje, ruke na leđa. After his retirement he served as the president of the Association of Croatian volunteer doctors 1990–1991.[7]