"After 20 or so years, we finally managed to get rid of this harmful legacy from the past," Culture Minister Daniel Herman told reporters.
The farm was constructed in the 1970s during Communist rule at Lety, a village south of Prague which was the site of a Nazi-era concentration camp where hundreds of people in the Roma and Sinti minorities died in 1942 and 1943.
The state bought the farm from the Agpi agricultural firm for 450 million koruna (USD 21 million) and will pay an additional 120 million koruna to clean the site.
The contract still needs to be approved at a general meeting of the firm, which is slated for December 4.
Another signatory to the agreement was Jana Horvathova, who heads the Museum of Romani Culture in the eastern city of Brno that will revamp the site after the pig farm is dismantled.
"Now the challenge will be to transform the site from a dishonourable place to one with dignity," EGAM president Benjamin Abtan told AFP.
About 1,300 Roma were interned at Lety from August 1942 to May 1943, and around 330, including at least 241 children, died there after a typhus outbreak.
Many inmates were later transferred to the Auschwitz- Birkenau complex where more than a million people are estimated to have been killed.
Under the Nazis, around 90 per cent of Czech Roma were exterminated.
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