The 27-year-old Fulham right-back, who plays in midfield for Bulgaria, has left the team's training camp in Pravets and will undergo a medical in Sofia to assess the extent of the injury he suffered on Monday.
Manolev, capped 29 times by the Balkan country, has scored twice in the qualifying campaign, against Italy and Armenia, and is one of the most influential players in Luboslav Penev's squad.
Bulgaria will play Malta at the Vasil Levski national stadium behind closed doors after their fans were found guilty by FIFA of racist behaviour in the qualifier against Denmark in October.
Unbeaten Bulgaria, who visit Denmark next week, have made a solid start to their campaign and are second in Group B with six points from four matches, four behind leaders Italy. Czech Republic are third with five points from three games.