The 19-year-old was initially denied re-entry into India after a mid-series break in the United Arab Emirates because he only held a single-entry electronic visa.
The issue is different to what Shoaib Bashir encountered last month and Ahmed was granted an emergency two-day visa, allowing him to train with his England team-mates in Rajkot on Tuesday morning.
Ahmed has now applied for a multi-entrance visa and England are confident the issue will be resolved before the series, currently deadlocked at 1-1, resumes on Thursday.
"We were advised, on returning to India, that there was paperwork discrepancy with Rehan Ahmed's visa," an England team spokesperson 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."
Bashir's arrival was delayed because of a unforeseen snag in his paperwork, with his Pakistani heritage leading to extended checks, and meant he missed the first Test win in Hyderabad last month.
Ahmed, like Bashir, was born in the UK and is of Pakistani heritage but he was already in possession of an Indian visa after being placed on standby for England's 50-over World Cup campaign.
That was not activated because he was not required to travel but, with all of England's team travelling on electronic visas which are not stamped on passports, any administrative issues are harder to spot.
Ahmed, England's youngest cricketer in all three formats, entered India for the first time ahead of the start of the series and has featured in both Tests, taking eight wickets at a decent average of 36.37.
He has also contributed 70 runs, including a cameo 23 after being bumped up to number three in the batting order as the so-called 'nighthawk' in the second Test, before England departed for the UAE.
Only when Ahmed had his passport scanned after England arrived at Hirasar Rajkot Airport following a chartered flight from Abu Dhabi did the oversight emerge.
England captain Ben Stokes and head coach Brendon McCullum remained with Ahmed while he was given his temporary stay and they arrived at the team hotel about an hour after the rest of the group.
England elected not to replace Jack Leach following his series-ending knee injury, leaving them with Ahmed, Bashir and Tom Hartley as the three specialist spinners, plus Joe Root's part-time off-breaks.
Any hitch in Ahmed's application process could diminish England's options even further but vice-captain Ollie Pope was upbeat that would not be the case.
"It all sounds pretty positive," Pope said. "We're getting around Rehan, he's in good spirits in training today.
"It was sorted fairly quickly yesterday but it's all going on behind the scenes and hopefully within the next day or so, it's all sorted."
