Police found the body of Aivar Rehe, 56, in his yard last Wednesday, two days after he had gone missing.
Rehe was the head of Danske Bank's Estonian branch from 2008 to 2015, two years before it found itself at the centre of a massive money-laundering scandal.
The bank is under investigation in Estonia, Denmark, the US, Britain and France, accused of helping launder about $230 billion (209 billion euros), primarily by Russians, through its branch in Estonia between 2007 and 2015.
“Police and prosecutors confirm that all evidence and information at our disposal points directly to suicide,” the prosecutor general's office told Estonian media, adding that a forensic doctor drew the same conclusion.
Rehe was not considered a suspect in the investigation. But Estonian police detained 10 other former employees of the bank last year and went on to charge them all with money-laundering.
Earlier this year, Rehe had said he thought the anti-money laundering measures taken by Dansk Bank had been sufficient at the time, but that he nevertheless felt responsible for what had happened.