He told reporters the two countries "maintain their anti-historic retrograde positions of not accompanying Argentina in its fight for the Malvinas (Falklands) and by rejecting Cuba's presence in these meetings."
Obama has said he hopes to turn around the U.S. decline in the region.
Before departing on his fifth visit to the region as president, Obama told Colombia-based Caracol Radio Friday morning that he wants to expand the "powerful trading base" the United States has with Latin America, which has some of the world's fastest-growing economies.
The American leader blamed Republicans in an "obstructionist" U.S. Congress for blocking immigration reform, to which he said he's committed.
U.S. Secretary of State Hillary Clinton noted on Thursday before leaving for Cartagena that the region's countries buy more than 40 percent of U.S. exports, three times as much as China buys from the United States in net value. The region also provides more than half of the United States' imported energy.
Nonetheless, the U.N. Economic Commission for Latin America and the Caribbean says a much greater share of U.S. exports, 61 percent, went to the region a decade ago. China has surpassed the United States in trade with Brazil, Chile, and Peru and is a close second in Argentina and Colombia.
U.S. assistance to the region has also decreased, with U.S. military, police and economic aid to Latin America falling from $3.2 billion in 2009 to a proposed $2.4 billion for fiscal 2013, according to a tally by three liberal think tanks including the Washington Office on Latin America.
The U.S. isn't the only summit participant facing challenges.
The Organization of American States, composed of all the countries in the Western Hemisphere except for Cuba, organizes the summit but has lost much of its former clout with the end of the Cold War.
The OAS, to which the U.S. still pays 59 percent of its $81 million annual budget, now faces competition from a hodgepodge of new regional groupings that have emerged this century, all of them omitting the United States and Canada. They include ALBA, a bloc proposed by Venezuelan President Hugo Chavez and including Cuba; the Brazil-inspired UNASUR, encompassing South America; and CELAC, comprising 33 countries including Cuba.
Nonetheless, the OAS still plays a prominent role in the region by coordinating institutions such as the Inter-American Commission on Human Rights, an important buffer against abuses that has recently come under attack.
Chavez, for his part, grabbed the spotlight at past summits but has not announced if he will attend this one. Chavez has been undergoing treatment for an unspecified type of cancer in recent months, traveling frequently to Cuba for treatment.
While other leaders were traveling to Cartagena Friday afternoon, Chavez was preparing to speak to his supporters from the balcony of the presidential palace in Caracas, marking the 10th anniversary of his return to power after a failed 2002 coup.
Vivian Sequera in Cartagena, Luis Alonso in Washington and Marco Sibaja in Brasilia, Brazil contributed to this report.
Follow Frank Bajak on Twitter: http://twitter.com/fbajak
Follow Vivian Sequera on Twitter: http://twitter.com/vsequera
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