Reports in the Indian media said the 19-year-old, who is of Pakistani heritage, had a single-entry visa but the England and Wales Cricket Board (ECB) said on Tuesday the player obtained a temporary visa and the correct one would be issued soon.
England won the first test before India levelled the series 1-1 last week, after which the tourists had a mid-series break before the next test which begins on Thursday.
"We were advised, on returning to India, that there was paperwork discrepancy with Rehan Ahmed's visa," a spokesperson for the ECB said.
"The local authorities at Rajkot Airport were supportive, enabling Rehan entry on a temporary visa.
"The correct visa should be processed and issued in the coming days. He will continue to prepare with the rest of the squad ahead of the third test."
England will hope the latest issue is sorted out quickly as they are already without spin spearhead Jack Leach for the remainder of the series due to a left knee injury.
Ahmed's fellow spinner Shoaib Bashir, who is of also of Pakistani heritage, was ruled out of the first test in Hyderabad due to a visa delay that was eventually resolved.
India and Pakistan have soured political relations and they do not play each other outside multi-team events. People of Pakistani origin are required to submit additional details to obtain an Indian visa. Australia's Pakistan-born opener Usman Khawaja had faced a similar visa delay before their tour of India last year.
The third test will be followed by matches at Ranchi and Dharamsala.
