He resigned to avoid Slovakia's ruling coalition crumbling apart.
Slovakia's health minister has resigned as part of a deal to defuse a political crisis over the purchase of COVID-19 vaccines from Russia.
Two parties in Slovakia's four-party governing coalition had called for Marek Krajci's resignation over his handling of the pandemic, in one of the EU's hardest-hit member states.
A political crisis was triggered last week after Slovakia signed a secret deal to buy 2 million of Russia's Sputnik V coronavirus vaccine, despite opposition from within the coalition.
Prime Minister Igor Matovic had defended the deal to buy the vaccines, saying it will speed up the vaccination programme.
But his coalition partners - the Freedom and Solidarity party and For People party - said the move cast doubts on Slovakia's pro-Western ideology and demanded the reconstruction of the government.
The European Medicines Agency launched a review of the Sputnik V vaccine last week but has not yet approved the jab for rollout in the bloc.
Krajci, from PM Matovic's Ordinary People movement, announced his resignation on Thursday in an effort to end the criticism.
"Two minor parties in the coalition have made my resignation a condition for their continued membership of the government," he told reporters.
"I don't want to obstruct in any way, so I am resigning from my position."
The prime minister described the resignation as a "painful" but correct decision because it prevented "a collapse of the government and early elections".
It was not immediately clear who will replace Krajci as Slovakia's new minister of health.
Slovakia has recorded more than 331,000 confirmed cases of COVID-19 and more than 8,244 deaths.
According to John Hopkins University, the 1.72 seven-day rolling average of deaths over the last two weeks in Slovakia is the second-worst result worldwide.
With the hospitals filled up with COVID-19 patients, the country asked other EU nations to send medical personnel to help with the situation.