The House voted to override Bush's veto 316 to 108, with most members unaware that a portion of the bill was missing.
"What we are dealing with is an unfortunate situation," said House Majority Leader Steny Hoyer (D-Md.).
Hoyer said that apparently the text of title 3 of the farm bill--a trade provision which Hoyer called "non-controversial,"--was left off the paper copy of the bill sent to the White House.
Although details on the path forward were not clear early Wednesday night, Democrats were expected to offer a resolution that would allow them to add Title III when the bill reaches the president's desk again.
Both chambers of Congress are expected to override Bush's veto of the massive $290 bill.
However, House Minority Leader John Boehner (R-Ohio) said the omission of a part of the bill could raise constitutional and legal issues.
"We may have transported to the president a portion of the bill, but we did not send the farm bill," said the Boehner on the House floor.
The Senate is expected to vote to override the bill on Thursday, although it is not clear what further action the House will take on the measure