But there's some concern the appointment of a former Canadian Forces boss might signal an impending militarization of the country's space program.
Natynczyk will officially take over as CSA president on Aug. 6, replacing ex-astronaut Steve MacLean who left unexpectedly last February.
Natynczyk retired from the military last year after serving four years as chief of the defence staff.
Jim Quick, the CEO of the Aerospace Industries Association of Canada, welcomed the appointment, noting that Natynczyk had a long record of distinguished service in Canada's military.
"The AIAC is very pleased that he has been selected to lead the CSA during this critical time," Quick said in a statement.
"The appointment is timely and encouraging given the pressing need to identify clear direction for Canada’s future in space."
The AIAC represents about 100 of Canada's aerospace companies which include MDA, the builders of the Canadarm; Lockheed Martin Canada Inc.; Magellan Aerospace and Telesat Canada.
Chuck Black, the treasurer of the Canadian Space Commerce Association, said Friday that he was a bit surprised by the announcement.
Black is glad the Harper government has announced its replacement for MacLean, but he added that Natynczyk faces a lot of challenges that include a shrinking CSA budget.
"I would hope it would lead to a little bit closer co-operation between the government and maybe some of the military space programs." Black said in an interview. His organization comprises 50 Canadian companies involved the space industry.
"I would hope that Natynczyk can add a bit of military discipline into the proceedings."
Geoffrey Languedoc of the Canadian Aeronautics and Space Institute said he expects Natynczyk to bring "an international perspective into the use of space assets for homeland defence."
The CASI executive director admitted the appointment also caught him by surprise for a couple of reasons.
"I didn't expect an announcement quite so soon," Languedoc said.
"And Natynczyk, in conversations that I've had, hadn't come up as a potential candidate. He wasn't on the radar screens of many people.
Steven Staples, the head of the Ottawa-based Rideau Institute, said Natynczyk's appointment raises questions about the future of Canada's space program and its closer relationship to the military.
"My concern is that we may be seeing the increased militarization of Canada's involvement in space," Staples said in a statement.
"Our role will move away from the scientific exploration toward the military exploitation of space."
Staples noted that the CSA's budget has been declining, while the military has been making significant space investments, including the Sapphire space observation and tracking satellite.
Sapphire, Canada's first military satellite, was launched earlier this year along with NEOSSat, (Near-Earth Object Surveillance Satellite) which is on the lookout for asteroids that cross Earth's path.
National Defence describes Sapphire as the largest part of the Canadian surveillance system, responsible for checking man-made space objects in high Earth orbit and for contributing to the U.S. Space Surveillance Network.
David Caddey, the executive vice-president of MDA, said he's happy the decision to appoint a new CSA boss was done quickly.
"It's not unusual for retired military to be appointed to these types of positions," he added. "If you look you can see that the administrator who is the head of NASA is ex-military."
Charles Bolden, NASA's administrator, had a 34-year career with the U.S. Marine Corps.
"I don't see this as a militarization of space," Caddey said.
"I think they're finding a well-experienced former military person and they're putting him in charge."
The MDA executive said what was needed is someone who understands Ottawa, and who can take directions from the government while leading an organization.
"I think he's first-rate to take us through these difficult times," Caddey said.
Caddey said Natynczyk's challenge will be to implement the Emerson report, which calls on the government to beef up spending to develop space technology.
David Emerson, the former cabinet minister who led the wide-ranging review, said Canada will lose its competitive position in the industry if it sits back and doesn't invest.
New Democrat MP Dan Harris, his party's deputy industry critic, called the appointment a surprise but he wished Natynczyk luck.
Harris, who is responsible for the CSA file, said Natynczyk's job will be more challenging because of looming cuts.
"By 2014, if things go as they're going, they'll be $40 million shorter on their budget which will make it much more difficult for the Canadian Space Agency to do what they do," he said.
Gilles Leclerc, who had been filling in as interim president, just recently had his mandate extended for 90 days until September.
The announcement of Natynczyk's appointment was made Friday by Prime Minister Stephen Harper as part of a broader shuffle in the public service.
Among others given new jobs was Margaret Biggs, who has run the Canadian International Development Agency since 2008.
Biggs had been leading the agency's merger into the Department of Foreign Affairs but will now join the Privy Council Office as a senior adviser.
Her replacement at CIDA will be Paul Rochon, a former associate deputy minister of health.
Note to readers: This is a corrected story. A previous version wrongly said NDP MP Dan Harris was the deputy defence critic
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