Analysts had estimated that stockpiles rose by 2.56 million.
The EIA's release followed data from the American Petroleum Institute on Tuesday which showed a draw by 7.6 million barrels, after markets had expected a build by about 1.5 million.
This surprise draw sent oil prices higher. Ahead of the EIA's release, West Texas Intermediate crude futures in New York were up 1.7% to $49.53 per barrel. WTI was last above $50 per barrel on June 29.