The former Reading winger has not played since the 3-0 defeat by West Ham on February 20 but remains the Tigers' top scorer with six goals.
The club were hoping Hunt would be fit to return last month but his recovery has not progressed as hoped and Hull have now admitted he will not be available for any of the run-in.
Saturday's woeful 4-1 defeat by Burnley left Iain Dowie's side four points from safety with five games remaining.
Republic of Ireland international Hunt had an exploratory operation on his foot yesterday, which revealed further damage.
Dowie told www.hullcityafc.net: "It's a big blow. Whenever you lose your top goalscorer it's going to be a blow.
"Stephen couldn't settle down and the pain returned. The surgeon had a look at it and decided to pin a little bone in there.
"It's disappointing for the lad. I spoke to him this morning and he is bitterly disappointed."
Hunt's injury has meant Dowie has not been able to pick the 28-year-old since replacing Phil Brown last month.
The former Crystal Palace and Coventry boss has been somewhat hamstrung in his selections because of the Tigers' lengthy injury list.
Dowie did receive some good news when tests showed defender Andy Dawson, who was carried off in the second half against Burnley, suffered only bruising to his leg.
The 31-year-old could feature against Birmingham on Saturday but Hull will definitely be without defenders Kamil Zayatte and Anthony Gardner, who may not play again this season because of knee and ankle problems respectively.
However, Dowie knows there is no time to bemoan his ill fortune.
"Hunt, Gardner and Zayatte have been great players for the team whenever I've seen Hull this season," he added.
"But we have to get on with things and we need some big players to step up to the plate against Birmingham on Saturday."