CO2 incubator provides not only the constant CO2 (usually 5%) but also adequate humidity level and gas exchange between culture and ambient atmosphere. You cannot simply pre-equilibrate media with CO2 and then keep it open to the atmosphere outside the incubator: excess CO2 will disappear in 5-10 min. The simplest solution is just to replace the porous caps on your culture flasks with the rubber stopper to keep 5% CO2 inside. But other conditions (temperature, humidity, absence of toxic volatile metabolites) should remain adequate.

Nicolai S Panikov Thank you for the answer. It is very helpful. We take care of the humidity and the temperature is maintained at 37degrees. The problem is 5% CO2 only because I am using bacterial infection and we have to use a separate incubator. I am using 10mM HEPES to compensate for that problem but I don't find that sufficient sometimes.

Yes, understand. It is a common problem of paranoia about infection. You can try to convince your colleagues as follows: place your flasks in the second container supplied with an anti-bacterial filter (pore 200 nm or less), wipe the container with 70% alcohol, and dry in BSC. Now it is safe to place it in a common CO2 incubator. Discuss the issue with the lab manager or PI. Good luck!