That comes on top of a 4.3 per cent increase for the 2011-2012 school year.
In comparison, inflation was 1.3 per cent between July 2011 and July 2012.
The agency says the average tuition bill this year is $5,581, compared with $5,313 a year earlier.
Tuition fees rose in every province except Newfoundland and Labrador, where they have been frozen since 2003-2004.
Undergrads in Newfoundland and Labrador and Quebec continued to have the lowest average fees, while Ontario students paid the highest tuition in the country.
With this year's increase, tuition fees in Quebec were $2,774, just above the $2,649 charged in Newfoundland and Labrador.
Ontario students paid an average of $7,180 in tuition.
Dentistry students paid the highest average undergraduate fees at $16,910. Medical students paid an average of $11,891 and pharmacy students paid $10,297.
All undergraduate programs saw increases, ranging from 2.7 per cent in agriculture, natural resources and conservation to 6.8 per cent in business, management and public administration.
Average tuition increases ranged from two per cent in British Columbia to 10.1 per cent in Quebec.