Morneau told CNBC he has spoken with Treasury Secretary Steven Mnuchin three times this week, showing the two sides' continued "ability to work together."
"There's an understanding that we trade together, that we're part of an integrated North America," he added.
Commerce Secretary Wilbur Ross, whose department recommended the tariffs, told CNBC shortly after Trump's signing ceremony: "There's no question that the action the president took today is a further motivation to both Canada and Mexico to make a fair arrangement with the United States."
Earlier in the week, Ross had forecast on CNBC that Trump would likely provide a degree of flexibility on tariffs for Canada and Mexico, a softening from the hardline plan the president unveiled last week. Ross on Wednesday said the White House is "not trying to blow up the world."
Trump on Monday had also dangled the possibility of dropping his call for steel and aluminum tariffs if NAFTA is renegotiated to terms more favorable to the U.S.
Regarding those talks, Morneau said Canada is working to get a better deal. He said Canada sees the trade agreement as helping both American and Canadian workers.
"Getting to a better arrangement, recognizing a whole host of economic issues that weren't the case 30 years ago ... it takes some working together and we are cautiously optimistic that we're going to get there," he said.