Out of I-League title race, East Bengal appointed the Santosh Trophy-winning coach on an interim basis, his tenure fixed till the Federation Cup.
With less than a month to go for the Federation Cup, the 56-year-old suffered the injury on his left foot.
"I've ruptured my Achilles tendon and will be out of action for at least four weeks. I wanted to give it all for East Bengal in the remainder season but such a big opportunity is wasted in such a cruel manner," an emotional Banerjee said after he was discharged from the hospital.
Banerjee was named coach less than 12 hours after Englishman Trevor Morgan shot off a resignation letter following a string of losses, including a humiliating defeat in I-League derby.
A 0-1 defeat to DSK Shivajians on April 16, their latest, meant their elusive I-League title hopes were dashed.
East Bengal are third on the table with 27 points from 16 fixtures, below title contenders Aizawl FC and Mohun Bagan.
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