Birds Point levee
The corps used explosives at the three points on the levee in May 2011 as floodwaters threatened nearby Cairo, Ill.
Phase two should be complete within a few days.
The breach allowed 130,000 acres of Missouri farmland to flood.
The corps said it received the letter a week ago protesting the contract to reconstruct the levee.
The levee was intentionally breached last year to alleviate flooding on the Mississippi River.
The class-action lawsuit was brought by more than 140 southeast Missouri farmers whose land was damaged when Birds Point levee was intentionally breached.
Corps officials say the decision to breech the Birds Point levee may have saved billions of dollars in damages.
The corps halted its floodway repairs in December after spending $20 million to shore up the levee to 55 feet of flood protection at each of the blasting spots.
After the intentionally breached in May
The program requires the levees to pass routine inspections and their operators to chip in 20% of the repair costs.