Natalie Huber with the Social Services ministry says 55 children were taken into care last month, more than double the average number.
She says hotels are used only under exceptional circumstances and, in this case, there were no spots with foster families, extended relatives or non-profit groups.
As of Friday, there were 13 children living in hotels in the capital city.
The Manitoba government has vowed to put an end to using hotel rooms as emergency placements for children after two teen girls living in them were attacked.
Huber says the case is a bit different in Regina, where most of the children are under 10 and are staying in hotel rooms with support staff.
"We're not seeing adolescents in these situations," she says.
"The care we're providing in these hotels — we're heavily supervising. There's 24-hour staff in the rooms."
Huber says plans were being made for six of the children still in hotels to move out and officials were working to find placements for the others.
She hopes the spike in numbers is an anomaly and they will go down.
"This is not something that we anticipate being long term. We're already in discussions about some ... options to move away from this."
Hotels have been used about six times in the last two years in Regina and North Battleford, she says.
Officials in Manitoba promised last fall to stop using hotels when 15-year-old Tina Fontaine ran away from her downtown Winnipeg hotel. Her body was found days later, wrapped in a bag in the Red River.
In April, another 15-year-old girl in care in a Winnipeg hotel was allegedly attacked by a male teen also being housed at the hotel. She remains in hospital.
Manitoba announced last week that it has virtually eliminated hotel use in Winnipeg, but not in some rural and northern areas.