"31 people have been killed between April 28 and May 4, more than three cases are to be confirmed," the institute said on late Wednesday.
According to the institute, the protests left 1,220 protesters injured, with 18 sustaining eye trauma. In nine cases, police officers resorted to sexual harassment toward women.
The largest number of fatalities – 24 – were registered in the western city of Cali.
On late Wednesday, a group of protesters tried to gain access to the Congress building as lawmakers gathered to discuss the rallies.
"Several minutes ago, we had to evacuate the Congress building to ensure safety as some protesters tried to rush inside. Let us not allow violence to drown out the protest!" lawmaker Mauricio Toro tweeted.
The politician called on protesters to keep restraint and stressed that Congress was working to protect democracy and the people's right for peaceful protest.
Security forces reportedly prevent protesters from entering the legislature.
The rallies in Colombia, against an increase in gas prices and utility bills as part of a state-proposed tax reform, have been underway since last week. Although President Ivan Duque called the reforms off on Sunday, marchers have continued to protest, calling for a nationwide strike.
In addition to the cancellation of the tax reform, labor and student organizations are demanding a review of the sanitary emergency and health care reform, the dissolution of the Esmad riot police, the demilitarization of cities and punishment for those who killed protesters.