The White House National Security Council said in a statement that progress has been in Rwanda since the 1994 genocide of 800,000 ethnic Tutsis and moderate Hutus.
"We remain concerned, however, about a series of disturbing events prior to the election, including the suspension of two newspapers, the expulsion of a human rights researcher, the barring of two opposition parties from taking part in the election, and the arrest of journalists," National Security Council spokesman Mike Hammer said in a statement.
The land-locked African country's stability and prosperity will be difficult to sustain without broad political debate and open political participation, Hammer said.
Critics say the Rwandan election campaign was marred by government repression. Human rights groups pointed to mounting violence during the run-up to the election after the fatal shooting of a local journalist and the killing of an opposition official who was found nearly beheaded in July. The government denied involvement.
"Democracy is about more than holding elections," Hammer added. "A democracy reflects the will of the people, where minority voices are heard and respected, where opposition candidates run on the issues without threat or intimidation, where freedom of expression and freedom of the press are protected."
The White House statement does not congratulate Kagame for his re-election in Monday's voting.
Kagame's nearest rival, Jean Damascene Ntawukuliryayo of the Social Democratic Party, won 5 percent of the vote, according to final election results released on Wednesday.
"We have expressed our concerns to the government of Rwanda, and we hope the leadership will take steps toward more democratic governance, increased respect for minority and opposition views, and continued peace," Hammer said