The group of about 5000 has travelled across the country in buses and utilities in a procession known as the minga - an Indigenous term for joint community work or action.

The Indigenous groups, most from the country's southwest, are complaining about mining concessions and growing violence that has accompanied setbacks in implementation of a 2016 peace deal between the government and Revolutionary Armed Forces of Colombia rebel group.

That accord called for improved infrastructure and aid for rural areas.

The problems have led to a rise in conflicts involving guerrilla factions, the army, drug traffickers and illegal miners, all of whom have been accused of trampling Indigenous rights.

The protests are demanding a resumption of peace talks with another, smaller rebel force, the National Liberation Army, that broke down several months ago.

Protest organisers also want the government to remove the military from indigenous areas and to improve safety for community and human rights leaders, more than 160 of whom have been killed this year in Colombia.

Duque has refused to hold an open meeting, saying debates about public policy should be tackled by congress.

The government says it already has invested $US190 million ($A268 million), for education and security in Indigenous areas, to meet demands by previous Minga demonstrations.

The minga's arrival in Colombia's capital comes a few days before other protests planned by union leaders and student groups as the nation's economy struggles to recover from the coronavirus pandemic.

Australian Associated Press