Sajjan called on Boeing to abandon the anti-dumping challenge it has launched against Canadian plane maker Bombardier, saying Ottawa was disappointed by the USA company's behavior.
Boeing insists the plane receives Canadian government subsidies that give it an advantage internationally.
Boeing's complaint also prompted Foreign Affairs Minister Chrystia Freeland to order a review of the planned Super Hornet deal, saying "there will be consequences" for Boeing.
"Boeing values Canada as a customer and supplier-partner, and we continue to seek opportunities to expand our current and future partnerships with Canadian industry, the Canadian government and the aerospace industry in Canada at large".
A Boeing F/A-18 E/F Super Hornet flies on display during Farnborough International Air Show, Farnborough, England, Tuesday, July 15, 2014. That includes 560 companies that provide parts to Boeing commercial airplanes and 2,000 company workers in the country.
"We're very disappointed with the actions Boeing has taken against Bombardier.We believe (Boeing's) position is unfounded", Sajjan said on the sidelines of the Shangri-La Dialogue, an annual meeting of global defense officials.
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"We strongly disagree with the decision of the United States Commerce Department to initiate a trade remedy case in response to Boeing's petition against Bombardier", Sajjan said.
Sajjan also made a pitch for the defence industry to help Canada with its broader agenda with the USA - keeping borders open to trade in the face of possible protectionist action by the Donald Trump administration. He emigrated with his family to Canada when he was five years old.
Canada had announced plans to buy 18 Super Hornet fighter jets as a stopgap measure to beef up its legacy fleet of CF-18 fighter jets - also produced by Boeing - because it didn't have enough jets to meet its NORAD and North Atlantic Treaty Organisation obligations, Sajjan said. It needs the eighteen Super Hornet jets as a stopgap until an open tender competition can be launched.
Steven MacKinnon, parliamentary secretary to Public Services and Procurement Minister Judy Foote, told reporters that Boeing "is not acting like a valued partner right now so we've suspended discussions with that partner".
This CADSI video explains what CANSEC is, Canada's Global Defence and Security Trade Show.