The Aston Villa midfielder sustained an Achilles injury in Saturday night's 1-0 win over Liechtenstein in Vaduz which took the Scots into second place, one point above Czech Republic.
The Scots now at least have to equal the Czechs' performance in Lithuania if they are to clinch a play-off spot.
The Scotland boss revealed other bumps and bruises within his squad and confirmed striker Kenny Miller, who missed the game against Liechtenstein with a groin injury, would be assessed but Bannan appears to be a new worry.
"Barry Bannan has a gash on his heel and he was uncomfortable this morning," said Levein. "It is a really awkward area.
"The doctor had to put some glue on it to hold it together.
"He is doubtful, but it is very soon after the game to get a clear picture of who is going to be available or not.
"Craig Mackail-Smith's back is bothering him a bit - and he has a history of that.
"There are quite a few niggles but we will get a clearer picture tomorrow.
"I haven't had the opportunity to speak to Kenny or the doctor but he is another who is in the wait-and-see category."
Source: Team Talk