"Initially when it was discovered on Saturday morning people were a little bit unsettled ... but as we went through the day and over the weekend, probably people have become a little bit more frustrated and disappointed," Mr Mark said.
"They just can't comprehend how or why someone would do that."
It was not yet known exactly how much money was stolen, but Mr Mark said it was unlikely to have been a significant amount.
"It would have been what we had received over the last couple of days [before Friday]," he said.
"But in charity space every dollar is something that you guard very jealously and that we are extremely thankful for, because it does come from the generosity of the communities that we serve, and you never like to see that generosity undermined in any way."
A security guard had been stationed at the house over the weekend to give families "peace of mind", he said, and a review of security measures would be conducted this week to "look at other areas where we can potentially improve and increase our coverage".
Police were investigating the burglary, Mr Mark said, and had conducted a forensic examination.
"Canterbury Police can confirm that an investigation is underway after a burglary was reported at Ronald McDonald House overnight on Friday/Saturday (24/25 July 2015)," Senior Sergeant Scott Anderson said in a statement.
"Initial indications are that a safe is missing from the property."
Investigations into the incident were ongoing, a spokeswoman said.
