John Baird says the five-year upgrade involves utilizing new technology to screen air cargo, Canada's National Post/Canwest News Service reports.
The screening will be done by shippers, freight forwarders and air carriers using newer and more effective technology, Baird said.
He added that 75 percent of commercial cargo travels on planes carrying passengers.
"We must remember that terrorism is not just something that happens somewhere else to someone else," Baird said. "Canada must prepare and remain vigilant."
Since the Sept. 11, 2001, attacks in the United States, airline passengers have been subjected to growing security regulations while Canadian rules for air cargo haven't seen many changes.