"Today we've agreed to several important steps to increase trade, improve our competitiveness and create jobs for both our peoples," Obama said at a news conference with Harper.
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"We agreed to a new vision for managing our shared responsibilities, not just at the border but beyond the border," Obama said.
Business groups in both countries, which are each other's biggest trading partner, have long voiced concern about the "thickening" of the 5,525-mile (8,900-km) U.S.-Canadian border due to security measures enacted after the September 11, 2001, attacks on the United States.
Two-way goods trade hit a record $600 billion in 2008, but slumped to $403 billion in 2009 after the global financial crisis sent the U.S. economy into recession.
Trade rebounded in 2010, renewing concerns about long wait times for goods to clear the border.
Harper dismissed concerns the increased cooperation with the United States on security issues posed a threat to Canadian sovereignty.
"It is in Canada's interest to work with our partners in the United States to ensure that our borders are secure and to ensure that we can travel and trade across them as safely and as openly as possible within the context of our different laws," Harper said.