The agency says this was the seventh monthly advance since the beginning of the year.
The September increase came from the residential sector, mainly in Alberta and Quebec.
The total value of residential building permits rose 3.3 per cent to $4.1 billion, following a 4.8 per cent decline in August.
In the non-residential sector, the value of permits edged down 0.8 per cent in September to $2.5 billion, the third decrease in four months.
The value of building permits rose in six provinces, with Quebec posting the largest advance, followed by Alberta.