Flood has undergone an operation after rupturing his left Achilles in last weekend's epic Heineken Cup semi-final victory over Cardiff Blues.
He is expected to take up to six months to regain full match fitness and the injury rules him out of the Tigers' push for the Guinness Premiership and Heineken Cup titles. He will also miss out on England's summer tour to Argentina.
"It is very disappointing news for Toby at the end of his first season with the club. We wish him a speedy recovery and look forward to welcoming him back into the squad," said Tigers coach Richard Cockerill.
Flood's operation means both Heineken Cup finalists will have to go into the game in Edinburgh on Saturday, 23 May without their first-choice outside halves. leinster's Felipe Contepomi damaged knee ligaments in his side's victory over Munster at Croke Park.