Allan McGregor has suffered a recurrence of the groin injury that almost saw him miss Saturday's opening game with Serbia when his heroics helped the Scots to a clean sheet and a point in the 0-0 draw.
Blackpool keeper Matt Gilks is also carrying an undisclosed injury. And today Levein drafted in St Mirren No.1 Craig Samson as emergency cover.
Levein also has concerns over midfield star Charlie Adam, but the Scotland manager says he is optimistic all three will be passed fit for the Macedonian match.
Levein said: "We have injury concerns over three of the lads. Allan McGregor has suffered a slight recurrence of the groin injury that he had prior to joining up with us for the Serbia game.
"It is nowhere near as bad as it was originally. We will be guided by our medical staff, but I am not anticipating the need for another injection, that is something that would be more appropriate from his club. But we are optimistic and so is Allan.
"However, Matt Gilks also has a slight problem so we have called in Craig Samson from St Mirren and he will take part in training today."
Levein added: "Charlie Adam also has a minor problem, but again I spoke with him earlier and we are optimistic that Charlie will be fine to take part."
The Scotland manager was also keen to put Saturday's 0-0 draw with the Serbs in perspective.
Levein said: "There has been a bit of an hysterical over-reaction.
"We have played one match and I feel that was a decent point against the Serbs and there are 27 points still to play for.
"If we can get the win against Macedonia we will have four points and if results go our way elsewhere we could be top of our group by Tuesday night.
"So it could well be that point and clean sheet against the Serbs could be a very good one down the line.
"But we are under no illusions that Macedonia will present us with a different type of challenge and it will be a tough one at that."
Meanwhile, Jordan Rhodes has vowed to repay Scotland fans for their support – by scoring the goals that breathe life into our World Cup qualifying campaign.
Frustrated Tartan Army foot-soldiers chanted the £8million striker's name during Saturday's game.
Levein finally threw the Blackburn Rovers hitman on with 10 minutes to go, but he was unable to make a difference.
Scotland could not break down their opening Group A opponents, but the 23-year-old is confident he can get on the scoresheet tomorrow night if he gets a chance.
He said: "It was good to be involved on Saturday. I won't forget the experience.
"It would be nice to go back and repay the fans, show their faith in me wasn't misplaced, by scoring some goals.
"I am looking forward to the Macedonia game. To be involved in that would be fantastic."
Steven Naismith looks likely to escape further punishment for elbowing an opponent on Saturday, an incident missed by the referee.