The president said she removed the IT and Foreign Trade Minister Marti Kuusik, at the request of the prime minister and gave no more details for the reasons.
Estonia's President Kersti Kaljulaid said Tuesday she had relieved a minister of the far-right party EKRE of his duties, just a day after the new government was sworn in.
The move came after police said they were investigating Kuusik following an Ekspress Group news report linking him to gender violence of which he has denied any wrongdoing.
"In addition to a horrible media attack against me the prosecutor's office decided to start a criminal investigation. In this situation, I cannot work as a minister. Also, the rest of the government cannot work normally," he said in a statement Tuesday evening.
Prime Minister Juri Ratas echoed his comments:
"In the current situation, the government could not really start its work and fulfill its program. Hence foreign trade and IT minister Marti Kuusik requested to leave his duties today," Ratas said in a statement.
Kuusik was one of five ministers of EKRE, whose anti-immigrant message helped the party more than double its support in a March election, winning broad support in poorer rural areas.
EKRE is the second largest partner in Estonia's new government which agreed in April on a 36-page coalition plan that includes some of the party's racist immigration policies and pledges that Estonia will not take in any refugees as part of a European Union-wide quota system.