Slovenian Health Minister Tomaz Gantar resigned after his party left the country's ruling centre-right coalition.
It comes as a blow to Prime Minister Janez Jansa during the COVID-19 pandemic. The prime minister said he would temporarily run the health ministry.
Gantar's party, the Democratic Party of Pensioners, or DESUS, announced it was pulling out of the coalition government in protest of the prime minister's populist policies.
Jansa has faced accusations of pressuring the media and curbing criticism in the traditionally liberal European Union nation but he has denied the accusations.
The remaining coalition parties still appeared to hold a slight parliamentary majority.
Jansa's government was formed in March following the resignation of Slovenia's previous, liberal prime minister, Marjan Sarec. The PM is a close ally of Hungarian Prime Minister Viktor Orban.
Jansa also backed US President Donald Trump's reelection while votes were still being tabulated.
DESUS party leader Karl Erjavec, a former Slovenian foreign minister, said the party did not want an "'Orbanization' of Slovenia, an autocratic system and the people to be afraid," according to Slovenia's public broadcaster.
Slovenia has reported a slight slowdown in new coronavirus infections following weeks of soaring case numbers. Authorities have imposed a curfew and other measures to contain the spread.