The Slovakian has not traveled with his side as they flew out to Prague on Wednesday ahead of the last-32 clash at Struncovy Sady after suffering with the flu virus for the past few days.
Viktoria holds a 3-0 lead from the first leg after a shock victory at the San Paolo last week, thanks to goals from Vladimir Darida, Frantisek Rajtoral and Stanislav Tecl.
Partenopei regulars such as Morgan De Sanctis, Hugo Campagnaro, Paolo Cannavaro and Lorenzo Insigne have made the trip to the Czech Republic, along with star man Edinson Cavani.
Hamsik was the victim of armed robbery in Naples earlier this week when the window of his vehicle was smashed by thieves, who made off with the playmaker’s Rolex watch.
The 25-year-old was unharmed in the incident.