England returned to India on Monday following their mid-series break in the United Arab Emirates, but Ahmed was initially told he could not leave the airport in Rajkot after border officials spotted that his visa, issued ahead of the tour, was only valid for a single entry.
The 19-year-old was subsequently granted an emergency two-day visa to allow him to train with the rest of the squad on Tuesday morning and, having now applied for the correct clearance, England are confident the issue will be fully resolved before the series resumes on Thursday.
"It all sounds pretty positive," vice-captain Ollie 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."
The build-up to the series was overshadowed by visa controversy, with fellow spinner Shoaib Bashir missing out on the chance to debut in the First Test after being forced to fly back to London to resolve a paperwork issue relating to his Pakistani heritage. While Ahmed is also of Pakistani descent, his hold-up is separate and appears to have been an oversight on England's part.
The teenager was granted an Indian visa last year after being named as a reserve for England's World Cup squad, but did not end up travelling to the tournament.
As a result, he was able to use the same paperwork to get into the country at the start of the Test tour, but did not possess the same multi-entry visa as the rest of the red-ball squad, whose applications were made knowing England planned to fly in and out of the country during the breaks in the five-match series.
"We were advised, on returning to India, that there was paperwork discrepancy with Rehan Ahmed's visa," the ECB said in a statement this morning. "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."
Ahmed has taken eight wickets across the first two Tests, as well as making several handy contributions with the bat, and is in contention to keep his spot in Rajkot after England decided against calling up a replacement for the injured Jack Leach.
Leach was ruled out of the rest of the tour over the weekend because of the knee problem that saw England field a novice spin attack of Ahmed, Bashir and Tom Hartley as India levelled the series at 1-1 in Vizag.
Early indications are that one of that trio could make way for an extra seamer this week, with first look at the surface in Rajkot revealing a covering of green grass.
"If it stays like that, there's every chance two seamers will be played," Pope told the BBC. "I don't want to give away too many secrets, but at the minute there's a little bit more grass on it. It looks like a pretty good pitch. We always like to make a decision here the day before the Test begins."
James Anderson is set to keep his place, with Mark Wood and Ollie Robinson pushing for recalls should England tweak the balance of their side.