The Copenhagen international financial crimes unit SØIK said its probe, launched in August, was now at an advanced stage that justified the move against the bank.
It was, however, "important to note that we are still at the beginning of our investigation", unit chief Morten Niels Jakobsen said in a statement.
Investigators in Denmark, the United States, Belgium and Britain have been looking into Danske's Estonian unit activities between 2007 and 2015, with the focus on 15,000 non-resident clients, including many Russians.
Danske has acknowledged that much of the approximately 200 billion euros ($230 billion) that went through the branch during that period may need to be treated as suspicious in origin.
The Danish prosecutors are charging Danske Bank with violating money-laundering laws between February 2007 and January 2016.
The ongoing probe will also determine whether criminal charges should be brought against individual members of Danske's top management.
The bank's CEO Jesper Nielsen said the lender would help prosecutors.
"We will, of course, cooperate with SOIK and make ourselves and the knowledge we have available in relation to the ongoing investigation," he said in a statement.
US ratings agency Moody's last month cut its long-term rating for Danske, saying the probe "has increased the probability that Danske will receive substantial financial fines".