In 1851, he was elected for the first time to the Legislative Assembly of the Province of Canada; he was eventually to serve a total of five terms representing Kamouraska.

In 1867 the British North America Act was passed, creating the Dominion of Canada, and Chapais became the first Minister of Agriculture.

At this time, he also switched to representing Champlain in the Quebec legislature, due to a scandal over electoral irregularities in Kamouraska.

As Minister, Chapais was in charge of more than simply agriculture: the department was also responsible for the import and export of animals, immigration, the census, patent administration and trademarks, public health, manufacturing, and the arts.

His new position of Receiver General for Canada was significantly less prestigious and powerful, requiring little more than making and accepting payments on behalf of the government.