Rubaale is a hotly contested constituency between Ms Naome Kabasharira and the State Minister for Gender, Mr Mwesigwa Rukutana.
Their camps have on several occasions clashed during the campaign season.
Mr Latif Ngonzi, the Electoral Commissioner registrar said that they plan to extend voting in the area to Friday.
Three people, have reportedly been arrested in connection with the incident.
Reports show that the ballot box was stolen after the truck that was hired to deliver voting materials broke down.
Meanwhile, voting has been closed and vote counting is currently underway at most polling stations across the country.
The exercise which was conducted between 7am and 4pm saw a number of hitches where voting was delayed due to reasons ranging from late delivery of polling material to faulty biometric machines.
At St Mbaaga Kiwatule Primary School polling station in Nakawa West Constituency, by 4pm the time voting was meant to end, voters were still queueing.
Reports also show that some voters are returning to polling stations to witness vote counting.