The two hospitals are among the biggest in Northern Ireland but pressure on services continues to mount.
A spokesperson for the Southern Trust said: “A number of planned surgical lists at Craigavon Area Hospital and Daisy Hill Hospital were cancelled on Tuesday and Wednesday due to extreme bed pressures.
“These included a small number of ‘red flag’ procedures.
“Emergency surgery continued as normal.
“We are very sorry for the inconvenience and distress caused to patients and we will do everything we can to re-schedule these operations as soon as possible, with priority given to the most urgent surgery.”
Earlier this year, the Department of Health asked Northern Ireland’s health trusts to make £70m in savings this year.
The Southern Trust were asked to contribute £6.4m.
However, it was announced earlier this week that the Department of Health have scrapped together £40m from other departments, giving the besieged NHS a temporary reprieve.