He also held the office of State Secretary at the Ministry of Environment of the Slovak Republic and Director General of the Social Insurance Institution.
He was a member of the National Assembly of the Slovak Republic for the first time in the 2002–2006 election period for the SMER party, which has been operating under the name SMER – Social Democracy since 1 January 2005; he was a member of the National Assembly Committee for Agriculture.
[2] In the subsequent 2006–2010 election period, he did not exercise his mandate as a member of the Parliament; in August 2006 he was appointed State Secretary of the Ministry of Environment of the Slovak Republic, an office he held until August 2008, when he was appointed Director General of the Social Insurance Institution (SIB).
He was dismissed from his position in 2010 by the government of Iveta Radičová at the suggestion of Jozef Mihál, but in 2012 the court ruled that this move was illegal and Muňko held the post of Director of the insurance company again in 2012–2016.
The move was described as a loan and motivated by "formal-legal reasons", to prevent the dissolution of the SNS caucus, after the departure of three of its members from National Coalition party (Rudolf Huliak, Pavol Ľupták, and Ivan Ševčík).