The ruling reverses an earlier decision to drop the case that the PM had received European Union subsidies.
The Supreme State Attorney in the Czech Republic has ruled that fraud investigations into Prime Minister Andrej Babis should continue.
The ruling overturns a previous decision in September to drop charges.
Babis had been under investigation on suspicion of receiving €2m in European Union subsidies to build a conference centre outside the Czech capital, Prague.
He has repeatedly denied any wrongdoing and has rejected several calls to resign over the investigation.
Speaking to the Czech daily newspaper, Pravo, Babis said "there is not the slightest reason" for him to step down.
In November, Babis also denied claims that his son had been sent abroad to avoid being called as a witness in a corruption probe.
On Friday, the European Commission said it had submitted audit results to Czech authorities for further investigation.
The allegations of fraud led to widespread protests in the Czech Republic, the largest in the country since the end of communist rule 30 years ago.
Although Babis' government, led by the populist ANO party, survived a no-confidence vote in June, pressure has been building from coalition partners and EU authorities for his resignation.