Prosecutors in Athens on Tuesday ordered a preliminary investigation into UNICEF in Greece over suspected corruption, according to judicial sources.
It comes after the head of the Greek branch Sophia Tzitzikou wrote to the prosecutor's office after noting "irregularities" in the organisation's finances since she took over two years ago.
UNICEF has frozen operations by the Greek team for 60 days until the situation is clearer.
In a statement last week, the organisation said it was terminating arrangements with its Greek committee "due to concerns arising out of a recent independent audit."
"UNICEF has concluded that the necessary reforms in the group will not be achieved and we have taken steps accordingly," it added.
It said it would be establishing new arrangements to continue its work.
The Greek branch, which has around 30 employees, took control of its financial situation in 2002 when it became a private NGO.
The UN children's agency has recently been heavily focused on the migration and refugee crisis, which has seen tens of thousands of children arrive in Europe.
In February deputy director of the international organisation Justin Forsyth quit following complaints of inappropriate behaviour, when the global aid sector was hit by a wave of sexual misconduct claims.