The Canadian Safety and Security Program will be based in Regina.
The government says the program will pull science and technology together with operations and intelligence to predict and prepare for everything from terror attacks to natural disasters and serious accidents.
The program will cost $43.5 million a year.
The agency will work with Defence Research and Development Canada to improve the country's ability to detect chemical, biological, radiological and explosives threats.
It will also work on border and transportation security, emergency management, surveillance and intelligence, cybersecurity, interoperability and critical infrastructure.
The program will promote collaboration between all levels of government, industry and academia, as well as professionals in emergency management and response, public health, law enforcement and intelligence.
Defence Minister Peter MacKay said the new agency will strengthen public security
"This new program provides Canada a technological advantage to cope with disasters, minimizing as much as possible their impact on the lives and livelihoods of Canadians," he said.