MacLean has announced plans to leave on Feb. 1 to assume a position in a new venture to be created by Mike Lazaridis, the former CEO and co-founder of Research In Motion
"During his tenure as president, he was devoted as an accomplished physicist, astronaut and administrator to advancing the Canadian Space Program," the agency said of MacLean in a statement.
Federal Industry Minister Christan Paradis thanked MacLean for his commitment to public service and to his efforts in advocating the value of space technology and exploration.
"Over his impressive career, Dr. MacLean has made significant contributions to Canada's leadership role in space," Paradis said in a statement. "As one of Canada's most accomplished astronauts and as president of the Canadian Space Agency, he has supported space innovation and demonstrated his passion for science literacy.
"I want to personally thank him for his dedicated work and wish him all the best in his future endeavours."
Several sources told The Canadian Press that the former Canadian astronaut would go work for the Perimeter Institute for Theoretical Physics in Waterloo, Ont., which was founded by Lazaridis.
But later Tuesday, a spokesman for institute said MacLean would be working for a new venture involving many groups tied to quantum physics in Waterloo. John Matlock added that the Perimeter Institute was part of the "innovation ecosystem" in the region.
The institute, which describes itself as a major centre for theoretical physics research, also issued a statement saying it was pleased the technology cluster in the Waterloo area had attracted someone of MacLean's calibre.
"We look forward to collaborating with him and other partners who are building the Quantum Valley," the statement added.
The space agency said in a news release on Tuesday that MacLean will lead a team pursuing breakthrough scientific research and development in the highly specialized field of quantum physics.
He was appointed president of the space agency in 2008 and his mandate was set to expire this coming September.
One of the original six Canadian astronauts, MacLean joined the Canadian Astronaut Program in 1983.
The accomplished physicist flew on Space Shuttle Columbia as a payload specialist in 1992.
MacLean, who is married with three children, went into space for a second time in 2006 when he worked on assembly of the International Space Station.