The new deaths were announced after five protesters were killed in clashes with security forces on Friday in central Bolivia, a political stronghold of exiled ex-president Evo Morales.
The Washington-based IACHR, a part of the Organization of American States, also recorded 122 wounded since Friday.
While the rights commission counts nine dead over the past two days, the official government tally remains at five.
Interim leader Jeanine Anez's cabinet chief Jerjes Justiniano told reporters Saturday night that he would ask for "forensic doctors to speed up their work," but did not confirm a higher toll.
Fierce clashes between Morales' supporters and police forces have been ongoing since Anez, 52, declared herself acting president on Tuesday.
The former deputy senate speaker took over the top job to avoid a power vacuum -- a move endorsed by the Constitutional Court.
The IACHR said it considers as "serious" her Thursday decree authorizing the armed forces to participate in maintaining order and exempting them from any criminal responsibility.
Morales, 60, said on Twitter that the measure gave "carte blanche and impunity to massacre people."
Unrest in Bolivia first erupted when Morales -- the country's first indigenous president -- was accused of rigging the results of October 20 polls to gain re-election for a fourth term.
He eventually resigned and fled to Mexico after losing the support of Bolivia's security forces following weeks of protests.