Turkish authorities used tear gas and water canons against demonstrators in Istanbul Wednesday after police officials said such riot-control measures would be used as a last resort.
The federation, known by its French initials FIDH, issued an open letter Thursday to Turkish Prime Minister Recep Tayyip Erdogan and Turkish President Abdullah Gul, expressing concern about the use of force by police.
FIDH said it was concerned with "systematic and repeated violations" of the right to free expression.
"Recent events only reinforce our concern that the government favors authoritarianism and repression in response to the legitimate concerns expressed by the protesters, rather than dialogue and consultation," the letter said.
The organization called on the Turkish government to guarantee the safety of protesters and to set up an independent commission of inquiry to investigate allegations of police abuse.
The U.S. State Department issued a security advisory Tuesday in response to the unrest in Turkey. It said there were widespread reports of violence and at least two deaths associated with the unrest.
Protests last week erupted over plans to raze a historic park in Istanbul.