The 35-year old computer programmer was also suspected of attempting to sell the 9 million files containing identification card data, addresses, tax ID numbers and licence plate numbers. Some files contained duplicate entries, police said.
Greece's population is 11 million.
"We are investigating what the source of the data was and how they were used by the man arrested, and also the possibility of him providing them to someone else," police spokesman Christos Manouras told reporters.
Police were also looking into whether the man had obtained the data files by hacking into a government server and whether he had an accomplice, officials said. The files were discovered after police raided his home.
No charges have been pressed yet and the man is expected to appear before a prosecutor later on Tuesday.