The development means that Rohan Bopanna will have to shoulder the burden of playing the doubles rubber apart from playing the singles, yet again.
There was no need to name a replacement as Vishnu Vardhan is already with the team in Tokyo as a reserve player.
It will be second straight Davis Cup tie, which Paes will miss due to injury. He had withdrawn from the World Group first round tie against Serbia in March due to a wrist injury.
Mahesh Bhupathi had also missed that tie in Novi Sad due to a groin injury. Paes had, last week, opted out of the US Open mixed doubles semifinals along with Russian partner Elene Vesnina after suffering back spasm.
"Leander is still in the US. I spoke to him last night and he is still unwell. He is certain to miss the tie. He had undergone an MRI scan and a clear picture on his injury will be known only in three-four days," Col Ranbir Chauhan, AITA Executive Director (Development), told PTI.
Paes and Bhupathi, who re-united early this year, make a formidable combination and were favourites for the doubles rubber of the tie, starting Friday.
The winner will move to the elite-16 nation World Group. India had entered the World Group after beating Brazil 3-2 but the 1-4 defeat against Serbia in the first round brought them back to the play-off stage.