Pillay said Rwanda and Uganda are suspected of harboring high-ranking members of the March 23 rebel movement from the Democratic Republic of Congo, many of whom are accused of committing grave human rights abuses.
"If they [rebels] continue to elude justice in neighboring states, they remain a security threat, hampering efforts for sustainable peace and development in the region," she said in a statement.
The U.S. government announced it sent special African envoy Russ Feingold to DRC to assess the situation amid renewed fighting in eastern DRC.
M23 took over parts of eastern DRC in late 2012.
Pillay called on African communities to stop "turning a blind eye" to the presence of rights abusers in their territories.
A U.N. peacekeeping mission in DRC is mandated to use force to help ensure peace in the country.
M23 rebelled in 2012, accusing the government of backing out on a 2009 peace agreement integrating rebels in to the national military.