Obama has said he would re-open negotiations over the agreement.
McCain says he opposes moves to "unilaterally re-open" Nafta, a free trade pact between the US, Canada and Mexico.
McCain had earlier visited Colombia - where he urged the US congress to pass a free trade deal between Colombia and the US - as part of a tour of Latin America aimed at boosting his profile and assuring the region and US voters of his foreign policy experience.
Analysts say the visit was also aimed at courting the US Latino communities, which comprise 15 per cent of the nation's population.
The Democrat-controlled US congress has stalled a free trade bill with Colombia following concerns over potential job losses in the US at a time when the nation's economy is in turmoil, as well as over concerns of rights abuses in the South American country.
Speaking at a news conference alongside Calderon, McCain praised recent US initiatives on border security, including the controversial border fence being built between the two nations.
He also urged the US to create a "temporary worker programme" in order to prevent illegal immigrants from crossing the border to find work.
The US congress approved $400m in aid last month to pay for drug smuggling surveillance equipment, the first instalment of the $1.4bn "Merida Initiative" package promised by George Bush, the US president.