Veteran seamer Tuffey suffered a bicep strain during Sunday's opening one-day international match at Guwahati, which New Zealand lost by 40 runs.
Coach Mark Greatbatch said Tuffery played with "some discomfort" in that match but was able to manage it.
"It's appears to be ok when he bowls but he's unable to throw without pain so he will return to New Zealand to for further assessment and treatment," Greatbatch said.
Greatbatch said a replacement player would not be called on from New Zealand.
His starting place for the second match at Jaipur tomorrow could be taken by captain and spinner Daniel Vettori, if he is deemed to have recovered from a back injury.
Otherwise Tim Southee or James Franklin shape as logical replacements.
