The 24-year-old, who has not been named, was arrested in Tallinn under suspicion of using a trojan virus to empty accounts.
Estonian officials have been investigating the alleged thefts for over a year and have said the amount stolen could run into millions of euros. If found guilty the man faces up to five years in prison.
"The last 12 months have seen a dramatic rise in the number of new viruses, worms and trojan horses designed to steal the keystrokes of innocent computer users." said Graham Cluley, senior technology consultant at anti-virus company Sophos.
According to Cluley the rise has been significant. "Our labs analyse approximately 15 new pieces of malware which include this sinister payload every day, compared to only five a day this time last year," he said. "Hacking gangs are actively hunting for vulnerable computers in order to steal information and empty bank accounts."
In March SC reported police in London foiled a $423 million cyber-heist on a Japanese bank.