"From today on, every battalion, every unit will have a division assigned to compile any accusations of misconduct on the part of any member of the armed forces," Uribe announced on Thursday.
Colombia has received billions of dollars in aid from the US to combat drug production and smuggling operations carried out by rebel groups in order to fund their operations.
The scandal will bolster critics of the $600 million-a-year Washington sends in aid - the largest amount sent to any country outside the Middle East.
The arrangement could change after Barack Obama takes over the White House in January.
US Democrats want new aid to focus more on economic development projects instead of military financing.
Nearly a decade ago the US and Colombia launched a $6bn aid package known as Plan Colombia to cut illegal coca production in half.
But a US congressional report released earlier in the week found coca production had increased by 15 per cent between 2000 and 2006, indicating Plan Colombia appeared a failure.
Democrats in the US congress have also been increasingly critical of Colombia's human rights record, and the staunch Bush-ally may face further aid cuts under Obama's administration.
The 11 men killed disappeared from their homes near Bogota earlier this year. Their bodies later turned up in mass graves near the border with Venezuela.
The father of one of the victims, Milciades Castro Rojas, told Al Jazeera: "They took them away and killed them to show that they are winning the war. That's what they do here, kill civilians saying they are guerrilla fighters."
Human rights groups allege the incidentis not isolated and say more than 500 civilians have disappeared while in military custody.
"The President has put the armed forces under pressure to show results, to show success in the war," Diana Sanchez, a Human Rights advocate, said.
She and other human rights activists have denounced the system whereby troops gain promotions measured by the number of fighters killed.
The UN high Commissioner for Human Rights, visiting Colombia last week, also called the army abuses "widespread and systematic".
Critics of the Uribe administration have acknowledged that Colombia's four-decade-old conflict has ebbed under his military push and the country has become safer on the whole.