Ford chief executive Mark Fields said it was "going forward" with its plan to shift production of small cars from its Michigan plant.
However, he repeated assurances that no jobs would be lost due to the move.
Mr Trump threatened during the election campaign to impose a tariff on car imports from firms like Ford.
He said companies which moved jobs abroad would be charged "a 35% tax when they want to ship their products back into the United States".
The president-elect also said he would build a wall with Mexico and renegotiate the terms of the North American Free Trade Agreement (Nafta), which includes Mexico.
But the Ford boss said a levy on car imports would hurt the US economy.
"A tariff like that would be imposed on the entire auto sector that could have a major impact on the US economy," Mr Fields told reporters at the Los Angeles auto show.
"I continue to think that the right policies will prevail because we continue to share the same objective which is a healthy and vibrant US economy," he said.
Ford has previously said it would shift production of its US-produced Focus and C-Max models to a new facility in Mexico by 2018.
Mr Fields said on Tuesday it was moving the Focus to make room for two new products in Michigan.
He also expressed support for free trade deals like Nafta, echoing comments from BMW chief executive Harald Krueger last week.
US carmaker Ford is pushing ahead with plans to move some production to Mexico despite a threat by President-elect Donald Trump to impose hefty tariffs.