Crude inventories were down by 46,000 barrels in the week to Dec. 21, a much smaller decline than the 2.9 million barrel decrease analysts had expected.
Crude stocks at the Cushing, Oklahoma, delivery hub rose by 799,000 barrels, EIA said.
Refinery crude runs fell by 58,000 barrels per day, EIA data showed. Refinery utilization rates fell by 0.3 percentage points.
"The report was modestly bearish, as crude oil stocks held steady versus expectations of a sizeable decline," said John Kilduff, a partner at Again Capital Management in New York. "Exports of crude oil rose to nearly 3 million bpd, which cut against the bearish crude oil inventory headline."
US crude prices were little changed after the data, with WTI futures up 10 cents to $44.73 a barrel as of 11:10 a.m. EST (1610 GMT), while Brent dipped 9 cents to $52.07 a barrel.
Gasoline stocks rose by 3 million barrels, compared with analysts' expectations in a Reuters poll for a gain of 28,000 barrels.
Distillate stockpiles, which include diesel and heating oil, rose by 2,000 barrels, versus expectations for a 529,000-barrel drop, the EIA data showed.
Net US crude imports fell last week by 411,000 barrels per day to 4.7 million bpd.
US production rose again to 11.7 million bpd, tying a record reached several times in recent weeks, though weekly production figures often vary from official monthly figures that are released on a lag.