The fans were injured a short distance from the England team hotel in the Slovak capital Bratislava on Friday.
The game, a Euro 2004 qualifying match, had been in jeopardy because of heavy rain but was given the go-ahead after a pitch inspection on Saturday afternoon.
Phil Holland, 31, from Worcester, was shot in the leg while Gareth Jones, 30, from Coventry, was shot in the throat.
He was undergoing surgery to remove a bullet, but is said to be in a stable condition.
Police said the manager of a bar in the city centre called a security service to help him remove about 60 England fans at around midnight on Friday.
Security guards opened fire and hit two men, said police spokeswoman Marta Bujnakova.
Security is being tightened up at the hotel, ahead of the match, which kicks off at 1830BST.
Cartridges
Police found 16 cartridges in the bar and have detained one security officer, but are still searching for two others.
The two men were treated in the doorway of the Carlton Radisson Hotel, where the England team are staying ahead of Saturday's game against Slovakia.
The chief executive of the Football Association, Adam Crozier visited the men in hospital and said security arrangements around the match would be reviewed.
A friend of Mr Jones, Andy Harvey, described the moment of the attack.
"We were walking towards the Carlton Hotel, where the England team are staying, just after midnight, looking for a taxi, when there was a bit of a slanging match between English and Slovakian fans, then suddenly six shots rang out.
"We ran for it, but Gareth pulled up saying, 'I think I've been shot'."
Police believe the shot had ricocheted into Mr Jones' neck and that he was "very unlucky".
Mr Jones said the operation he was due to undergo was "quite straightforward".
The situation calmed down after police sealed off the square.
Slovak police say they will be working with British colleagues in Bratislava to try to catch those responsible.
A British Embassy spokeswoman confirmed two English fans had been injured.
Mr Crozier said there were no reports of other disturbances and the two fans appeared to have been "innocent victims".
Hooligans
The embassy spokeswoman said about 400 England fans had arrived in Bratislava and other supporters were gathering in Vienna, Prague and Budapest.
The spokeswoman said 4,000 fans with tickets were expected, and between 1,500 and 2,000 more were seeking to buy them in the city.
Police said that 16 suspected football hooligans had been stopped at airports on Friday ahead of the game.
The match is England's first qualifier for the 2004 European Championships.