The energy efficiency – indoor air quality dilemma is a common predicament in many buildings undergoing energy efficiency improvements. The main goal of this research is to study the impact of this dilemma on national final energy consumption and greenhouse gas emission reduction. A simulation using a system dynamics model was carried out. The stock of public buildings was split into four sub-categories based on when the buildings were constructed. Natural ventilation is used in all buildings before renovation. After implementing energy efficiency measures, two scenarios are simulated: one with and one without mechanical ventilation. Buildings constructed between 1940 and 1992 exhibit the greatest increase in both floor areas with energy efficiency measures and profitability ratio. The simulation results show that if ventilation is operated according to national building standards, total energy consumption in public buildings increases by 1.3 % in 2014 and by 2 % in 2040 compared to the situation where there is no mechanical ventilation. If the implementation of the energy efficiency measures is increasing at higher rate, the difference between both alternatives is increasing more. Energy efficiency measures in public buildings reduce national energy consumption and greenhouse gas emissions. However these measures also reduce indoor air quality thereby causing losses of productivity of the building occupants.