The low-key reorganization will place responsibility for the Canadian Food Inspection Agency with the Health Department, alongside the Public Health Agency of Canada.
The government says the move will bring the three agencies responsible for various facets of food safety under a single minister.
It says the move will strengthen the whole food safety process.
The food inspection agency has handled a number of crises in recent years, including the deadly listeria outbreak in 2008 and the massive 2012 recall of contaminated beef from the XL Foods plant in Brooks, Alta.
Some of the agency's non-food activities, including economic and trade issues and some animal health and plant protection work, will remain with Agriculture and Agri-Food Canada. A news release says the CFIA will continue to support the Minister of Agriculture and Agri-Food in exercising these responsibilities.
In the release, the Conservative government says the move will bolster Canada's public safety system as a whole.
"This will ensure clear focus, easy collaboration and timely communication with Canadians when it comes to food safety," the news release said.
"This change also further underscores the CFIA's commitment to food safety as a top priority."
The NDP, which has long criticized the inspection agency for not doing enough to prevent outbreaks, said the change in responsibility is merely cosmetic.
"We need more than just a change of ministers, we need a change of direction,” said NDP agriculture critic Malcolm Allen.
"The real test will be whether the new minister acknowledges past Conservative mistakes and presents a plan for fixing the mess the Conservative government has created.”
The food-safety system is a three-way operation.
Health Canada develops food safety standards and policies and participates in public awareness campaigns about safe food practices.
The food inspection agency checks that industry meets federal food safety and regulatory requirements.
The public health agency steps in when outbreaks occur, gauging the scope of the problem, providing epidemiology services and advising people how to protect themselves.
Note to readers: This is a corrected story. An earlier version had a wrong date for when the listeria outbreak that is referenced occurred.