In 1990 he became its vice-chairman and held this position until the dissolution of Czechoslovakia, becoming the first vice-president of the newly established Czech Statistical Office.

He appeared to be groomed to replace the long-time president Edvard Outrata who retired in August 1999; however the Social-Democratic government brought in an outsider Marie Bohatá from the academia.

In 2001 he participated in an International Monetary Fund mission exploring possibilities of establishing a statistical bureau in East Timor.

Since March 2002 he was a chief of research institutes at the Faculty of Informatics and Statistics of the University of Economics, Prague.

After Bohatá resigned due to a scandal with a huge error in foreign trade balance, Fischer was appointed president of the Czech Statistical Office on 24 April 2003.

[7] After the vote of no confidence of Mirek Topolánek's centre-right government in March 2009, in the middle of Czech Presidency of the European Union, Fischer was proposed to be the prime minister in April.

Fischer decided to remain in the government, where he proved very popular, until then although the parties offered him a post in the European Commission.