Here are some links to Master of Religious Education programs and other relevant graduate programs offered in Ontario. If you know of others please let us know.
St. Augustine’s Seminary, Toronto http://staugustines.on.ca/cms/One.aspx?portalId=90833&pageId=100581
University of St. Michael’s College in the University of Toronto, Toronto http://stmikes.utoronto.ca/theology/programs/basic-degree/#Master_of_Religious_Education_MRE
St. Jerome’s University – University of Waterloo: Master of Catholic Thought https://www.sju.ca/mct
St. Paul’s University-University of Ottawa: Masters of Religious Education and other programs http://www.grad.uottawa.ca/Default.aspx?tabid=1727&page=SubjectDetails&Kind=M&SubjectId=99
Links to other Religious programs and undergraduate and graduate level are found at http://www.canadian-universities.net/Universities/Programs/Religious_and_Theological_Studies-Ontario.html