Netherlands-based LeaseWeb announced it had deleted all Megaupload files from 630 servers.
LeaseWeb said in a statement it hosted the data for over a year at its own expense without receiving any requests to access it or retain it before deciding the time had come to use the servers for other purposes.
But Dotcom said in a series of Twitter posts that his lawyers repeatedly asked LeaseWeb to keep the data pending U.S. court proceedings.
Dotcom said that millions of users' personal files had been lost in the "largest data massacre in the history of the Internet."
U.S. authorities shut down Megaupload last year and indicted Dotcom and other executives. Prosecutors accuse them of racketeering by facilitating massive copyright fraud. Dotcom says he's innocent and can't be held responsible for those who chose to use Megaupload to illegally download songs or movies.
LeaseWeb's deletions would mostly affect former Megaupload users in Europe. Other Megaupload files remain stored on U.S. servers.
U.S. attempts to extradite Dotcom from his home in New Zealand have been delayed as his complex legal case plays out. His extradition hearing is now scheduled for November.
Dotcom this year started a new site called Mega. The deletions do not affect that site.