About 100 England supporters with tickets for Sunday's game are known to be planning to set off on a two-day train journey, changing trains in the Romanian capital, Bucharest.
The Moldovan authorities had informed the Football Association that supporters with tickets could pick up their visas when they reached the border and then travel on to Kishinev.
However, officials at Lancaster Gate have now been told that unless fans turn up at the border with visas already stamped, they will be denied access. "We were originally told that there wouldn't be a problem, but at the 11th hour we've found out that there could well be one." Steve Double, an FA spokesman, said. "The fans who haven't got visas yet must get one from the Moldovan consulate in Bucharest before boarding the train for Kishinev."
Double added that the FA was doing all it could to help supporters get to the game at the 20,000-capacity Republican Stadium. "We've appealed to the British embassy in Bucharest. If we hadn't, then fans arriving after Friday afternoon simply wouldn't have been able to get their visas," he said.
"The embassy has persuaded the Moldovan consulate to agree to open on Saturday. It will be open from 8am to 7pm local time to deal with visas. We're aware that some fans might already be en route, and won't know about this, and we don't want fans going all that way only to get stranded.
"The embassy has also stuck up posters in English at Bucharest station telling the fans what they have to do, but I must stress that unless supporters have a visa their chances of getting in are remote."
Richard Rufus, the Charlton defender, has become the latest player forced out of the England Under-21 squad for their opening European Championship qualifying match in Moldova on Saturday.
Peter Taylor, the coach, had already lost Nicky Butt, the Manchester United midfielder, Chelsea's Jody Morris and the Queen's Park Rangers striker Kevin Gallen from his chosen squad of 19.
And yesterday, Taylor, who has called up the Everton youngster Michael Branch as striking cover, was forced to rule out the Charlton centre-half. An FA spokesman, Clare Tomlinson, said: "Richard had a scan on his knee and unfortunately he's had to go home. But the good news is we expect Emile Heskey of Leicester to be fit after the treatment he has had on his hamstring injury."