Chief Glenn Hudson said 13 homes have been affected so far but he said more homes, between 12 and 20, are being evacuated Saturday.
He said the Fisher River is running high and he doesn't believe it has crested yet. He blames the flooding on ice jams.
Hudson said the evacuees have been sent to hotels in Winnipeg but he's worried because some of them have health issues such as diabetes and breathing problems and one woman is pregnant.
"Some of them were able to walk out with hip waders," he said. "And some just left their vehicles parked away from their home and ending up walking out on their own basically."
The CBC's Katie Nicholson reported that the Peguis Flood EMO centre was in full swing Saturday responding to multiple emergencies on reserve.
Co-ordinator William Sutherland told her as many as 400 homes are at risk of flooding in the community.
Officials said 60 flood evacuees had registered with the centre as of mid-day Saturday.
On Friday, the province said it had delivered 100 water tubes to Peguis and were being used at a number of homes threatened by flooding.
Hudson said 200 of the community's residents are still off reserve due to floods in 2009, 2010 and 2011.
Below is video the CBC's Jacques Marcoux shot of EMO co-ordinator William Sutherland putting on hip waders Saturday as he attends to emergencies around the community. Below that, the CBC's vehicle kicks up water as it drives along a flooded road Saturday.