Uganda has persistently violated the rights of its citizens and media in the aftermath of last month's presidential election which saw President Yoweri Museveni retain his hold on power, the United States said.
The comments are the latest sign of deteriorating relations between Western powers and Uganda, a vital ally in the region.
US State Department spokesman John Kirby said in a statement on Friday that Uganda's repeated detention of opposition figures and harassment of their supporters, and the government's interference in a challenge of the poll results are "unacceptable activities in a free and democratic society".
"The United States and Uganda have a long standing and strong partnership that has contributed to the stability and prosperity of the region," the statement said. "We are concerned that the Ugandan government's recent actions could endanger the economic and political progress that has enabled our relationship to grow."
Uganda's electoral commission declared Museveni, 71 and in power since 1986, the winner of the Feb. 18 election with 60 percent of the vote.
Kizza Besigye, who came in second with 35 percent and has rejected the results as fraudulent, has been under virtual house arrest for weeks. A second challenger, former prime minister Amama Mbabazi, has filed an official challenge to the results.
Mbabazi said his lawyers' offices were raided soon after filing the challenge. The government has denied any involvement.
Museveni has endeared himself to the West by contributing thousands of troops to a peacekeeping mission in Somalia. He has also been credited with bringing relative peace and economic growth to Uganda, a prospective oil producer.
But critics say Museveni has not done enough to raise more Ugandans out of poverty or address widespread corruption.
Monitors from the European Union (EU) have criticised Uganda for creating an "intimidating atmosphere" around the vote and have said the electoral body lacked transparency and independence.