The hospital, in a statement on Monday evening, warned families should seek alternative care where possible given it was dealing with more than 90 patients in its emergency department.
The demand was "unprecedented" with a high number of extremely unwell children, a hospital spokesperson said.
"We will always treat the most seriously ill children first which unfortunately means some patients with less serious conditions may experience longer wait times," they said.
More than 50 per cent of the patients that arrived on Monday afternoon were triaged as lower urgency, the spokesperson said.
"We anticipate wait times for these less seriously unwell patients will potentially reach more than 12 hours this evening."
It was unsafe to discharge patients from the hospital to free up beds given the severity of their conditions, the spokesperson suggested, although it had adjusted its inpatient wards where it was safe to do so.
The hospital put out a call to unrostered staff to help with the situation, and some had volunteered to work extra shifts.
The hospital urged families to contact the Nurse on Call service, the Victorian Virtual Emergency Department, and consider online telehealth options.
However, those with critically ill children should always call triple zero, the spokesperson said.
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