The first Joint Strike Fighter should be delivered in 2016.
The F-35s will replace Canada's CF-18s, which are due to reach the end of their working lives in about 2020.
MacKay brushed off criticism from opposition legislators who said the planes were too expensive and questioned why Lockheed Martin received a sole-source contract.
"This is the best aircraft we can provide our men and women in uniform ... This is one of the largest defence procurement projects in Canadian history," MacKay told a news conference.
The C$9 billion contract also covers weapons, training and equipment.
MacKay said media reports of a separate C$7 billion 20-year maintenance deal were wrong and an agreement would be concluded once the jets started going into production.