Prasek owned a nine-year-old lion and a lioness he used for breeding.
The cats were shot dead by police called to the scene in the village of Zdechov, in Vsetin District in the Zlin Region the bbc reported.
Mr Prasek, 33, bought the lion in 2016 and the lioness past year, and kept them both in home-made enclosures in his back yard in the village of Zdechov.
He was breeding them illegally and had been fined in the past because he did not have planning permission for the cages.
Police were alerted to the incident by Prasek's father who saw his son's body lying inside the enclosure through a security camera.
In response, Prasek reportedly refused to allow anyone representing the local authorities onto his property, leaving the two sides at an impasse. The animals were in separate enclosures, but and had drawn some concern from the residents in the past. It was gathered that he had bought the lion in 2016 and the lioness in 2018.
A lack of alternative facilities in the Czech Republic, or any evidence of animal cruelty, also meant the lions could not be forcibly removed. Police at the time deemed it a traffic accident.
In June, Prasek's female lion made headlines after she attacked a cyclist while on a walk on a leash. The cyclist was hospitalized for his injuries.
"Today's incident will perhaps finally help to resolve this long-term problem", said Zdechov mayor Tomas Kocourek.