Woakes sustained a tear in his right quad during the second Test against Pakistan in Leeds, but an ECB statement suggested it was caused in part by "a flare-up of a chronic right knee problem".
"Woakes has had an injection for the knee issue last Monday and will now undertake a rehabilitation and conditioning programme to address both injuries. A date for return cannot be specified at this stage, but he will not be available before the ODI series against India," the statement read.
Woakes' condition will be reassessed ahead of the ODI series against India that starts on July 12, which means he will be out of the preceding three-match T20 series against Virat Kohli's men.
However, there is better news of both Stokes and ODI skipper Eoin Morgan.
Morgan, who missed Saturday's game against Australia in Cardiff due to a back spasm, took part in training at Trent Bridge on Monday morning and hopes to play the third ODI on Tuesday, while Stokes is said to be "progressing well" after sustaining a torn left hamstring a couple of weeks ago.
"Stokes can bat fully and is now able to run at 90 percent capacity. He will commence his return to bowling programme this week," the statement said.
Stokes will be with the squad for the fourth and fifth ODIs in the hope that he is fit to play in the T20s against India in July.
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