The organization blamed guerrilla groups, the security forces and paramilitaries for the abuses – which include killings, enforced disappearances and kidnappings, threats, sexual abuse of women, recruitment of child soldiers, forced displacement and persecution of Indigenous leaders.
"Indigenous Peoples are increasingly under attack in Colombia," said Marcelo Pollack, Colombia Researcher at Amnesty International. "They are being killed and threatened, forced to participate in the armed conflict, and being kicked out of their lands."
"It is time for the Colombian government to take its obligations seriously and take immediate action to protect Indigenous Peoples."
According to figures from the National Indigenous Organization of Colombia, at least 114 Indigenous women, men and children were killed and thousands forcibly displaced in 2009 alone.
Amnesty International also said crimes committed against Indigenous Peoples are rarely investigated by the authorities.
Thousands of Indigenous Peoples have been forced off their land because they often live in areas of intense military conflict and rich in biodiversity, minerals and oil. Many other Indigenous communities have been unable to leave their territories because armed groups have laid landmines in surrounding areas.
Access to food and essential medicines has also been blocked by the warring parties, who often argue such goods are destined for the enemy. All parties to the conflict have occupied schools and used them as military bases, while teachers continue to be vulnerable to physical attack, denying Indigenous communities access to education.
"Unless the authorities take speedy action to protect Indigenous Peoples in Colombia there is a real risk that many will disappear," said Marcelo Pollack.
The Awá Indigenous People accounted for more than half of all killings of Indigenous Peoples during 2009.
They collectively own the land and rivers of the resguardo (Indigenous reservation) of El Gran Rosario in Tumaco Municipality, in the south-western region of Nariño.
The area is of strategic importance for the parties to the conflict. FARC and ELN guerrillas, paramilitary groups, the security forces and drug-trafficking gangs are all active in the area.
On 26 August 2009, 12 Awá, including six children and an eight-month old baby, were killed and several more injured by gunmen wearing military uniforms and hoods who attacked the community at 5am. Among those killed were Tulia García and her sons. Tulia García had been a witness to the killing of her husband, Gonzalo Rodríguez, by army soldiers on 23 May 2009 and had subsequently received threats.
Following the August massacre, 300 Awá, including 100 children, fled to the town of Tumaco, leaving their homes, belongings and livelihoods behind. Weeks after arriving in the town, people were still living in shelters they had built themselves or sleeping out in the open. Food and water were scarce and there were no sanitation facilities.
On 4 February 2009, 15 Awá, including two pregnant women, were killed by FARC guerrillas in Barbacoas Municipality in the department of Nariño.
Amnesty International called on those participating in the conflict, including guerrilla groups and the Colombian security forces, to respect the rights of Indigenous Peoples not to be dragged into hostilities and to respect the territories in which they live and depend upon for their livelihoods.
Colombia's 40 year long armed conflict has affected millions across the country and left tens of thousands dead, tortured and forcibly disappeared. The vast majority of victims are civilians.
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