The guidelines recommend opening windows and doors to allow natural airflow throughout the room.
When it comes to cold days, they recommend schools pre-heat rooms before school starts before letting the fresh air in.
On wet and windy days, they recommend partially closing windows while still "having a perceptible breeze travelling through the space".
Carbon dioxide monitors, supplied to schools by the ministry, should be used to determine the effectiveness of ventilation and schools should adjust their approach as needed.
Otago Primary Principals Association president Vicki Nicolson said the guidelines posed a dilemma between staying warm and having good airflow.
At Port Chalmers School, of which she is principal, staff would spend time testing, using a CO2 monitor, to see how much airflow was needed to reach safe levels of ventilation.
The needs of every school were different, and those in the north would be facing different problems to the south.
Dunedin could have long periods of cold and it was hard to know where the cutoff point for closing the windows should be.
"Schools were not built with Covid in mind."
Associate deputy secretary, property delivery, Sam Fowler said ventilation played an important part in minimising Covid-19 spread.
The ministry had sent out more than 2500 CO2 monitors to schools and more were to be sent out in term two.
The data collected would help determine what the right approach to ventilation was for them.
About 130 schools had sought support with ventilation from the ministry.
More than 400 portable air cleaners had been distributed to about 330 schools for use in areas having higher airborne transmission risk, such as staff rooms, music rooms or meeting rooms.
Seven of those schools were based in Otago and Southland.
All schools were expected to receive air cleaners in May.
The ministry was working to identify further suppliers of air cleaners, which would enable it to respond to the individual needs of schools, such as those in colder climates with limited ventilation options.
