The fires at St Ann's Church and the Chopaka Church began within in an hour of each other in British Columbia.
Officers said both buildings were completely destroyed, and that they are treating the fires as "suspicious".
Last Monday two other Catholic churches in the province were destroyed in fires, as Canada marked National Indigenous People's Day.
"The investigations into the previous fires and these two new fires are ongoing with no arrests or charges," RCMP Sgt Jason Bayda said.
It comes as hundreds of unmarked graves have been discovered at sites of former residential schools in Canada.
The government-funded compulsory schools were run by religious groups in the 19th and 20th centuries with the aim of assimilating indigenous youth.
Indigenous groups have demanded a nationwide search for more graves.