Pradeep, who had taken six wickets in the opening Test, had bowled only four balls with the second new ball yesterday and did not take field today.
The fresh injury blow to the hosts means that they have services of just one medium pacer, Dimuth Karunaratne, in the ongoing second Test.
"Nuwan Pradeep's out for one or two months," Karunaratne said at the press-conference after second day's play.
"We played only with one pace option, so when they asked me if we need to bowl a few overs with the new ball, I said I could. That's why I bowled a few overs with Chaminda Vaas to see how it goes."
Pradeep could bowl only 17 overs on the opening day. He had left the field complaining of a hamstring niggle.
Sri Lanka is already going through a tough phase due to injuries to their key players. All-rounder Asela Gunaratne was ruled out of the three-match series after he broke his thumb in the Galle Test.
India had defeated Sri Lanka by 304 runs in the first Test.
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