Colombia's death toll from Covid-19 passed the 100,000 mark on Monday with a new 24-hour record of almost 650 deaths, the health ministry said.

After three weeks of demonstrations that have brought thousands of people into the streets to protest the government of conservative President Ivan Duque, the South American country of 50 million is suffering its worst moment since the pandemic began.

It has now recorded 100,582 dead, including 648 in the past 24 hours, the ministry said.

In proportion to its population, Colombia is reporting the fourth worst death toll in Latin America and the Caribbean, and the sixth for the number of infections, according to an AFP count.

"More than 10,000 deaths could have been avoided if we had not had these gatherings in the past six or seven weeks," Duque said in a statement.

Colombia has recorded over 100,000 deaths from Covid-19
Colombia has recorded over 100,000 deaths from Covid-19 AFP / Raul ARBOLEDA

The health authorities identified a resurgence of the virus in early April, and brought in restrictive measures such as a nightly curfew in the main cities.

But since April 28, thousands of Colombians have turned out to protest in the street, spurred on by a heavy-handed police response, even after the government scrapped the controversial tax hike that sparked the demonstrations.

On Monday, authorities in Bogota reported that one person had died during fresh clashes between police and demonstrators.

Government secretary of Bogota Luis Ernesto Gomez identified the victim as Jaime Alonso Fandino, 32, saying in a video posted to Twitter that the doctor who treated him said Fandino "was hit in the chest with a blunt object most likely at very close range."

Images released by local authorities showed members of the riot police using stun bombs to disperse protesters armed with stones.

According to civilian authorities and the ombudsman's office, at least 63 people have been killed in clashes since the start of the protests.