Two other small blasts, caused by crude devices according to Agence France-Presse, went off near the US Embassy in Bogota, the Colombian capital.
Separately, a scandal involving the Secret Service also overshadowed the start of the sixth Summit of the Americas in Cartagena.
Reuters cited police as saying the blasts may have been a protest by leftist guerrillas against the presence of Obama at the meeting.
"Nobody was killed, nobody was injured, and there was no damage," a police official told AFP.
More than 30 presidents and prime ministers are attending the talks, which will focus on the drug wars in the region, as well as on Cuba, AFP reported.
Specifically, the issues to be addressed will include drug legalization and Cuba's continued exclusion from the summit, as well as trade, the relevant economies, and energy.
Before leaving Washington, Obama told an association of leading Latin American newspapers that he rejected the idea of decriminalizing drugs.
Washington would not "legalize or decriminalize drugs because doing so would have serious negative consequences in all our countries in terms of public health and safety," he reportedly said.
On Cuba, he said that Havana authorities "have shown no interest in changing their relationship with the United States, nor any willingness to respect the democratic and human rights of the Cuban people."
The blasts did not affect preparations for the summit nor the dinner between Obama and his host Colombian President Juan Manuel Santos late Friday.
However, within hours of arriving, an undisclosed number of Secret Service agents traveling with the president had been relieved of duty and replaced.
"There have been allegations of misconduct made against the Secret Service in Cartagena, Colombia, prior to the president's trip," said Edwin Donovan, an agency spokesman, in a statement reported by CNN. "Be
cause of this, those personnel are being relieved of their assignments, returned to their place of duty, and are being replaced by other Secret Service personnel. The Secret Service takes all allegations of misconduct seriously."
Donovan declined to identify the nature of the alleged misconduct, saying it would be handled by the agency's internal affairs.