But in the talks in the ancient city of Samarkand, he tempered any public criticism as he sought deeper US ties with the region seen increasingly as lying in the shadow of an assertive Russia and exposed to Islamist militancy.
Kerry was in Samarkand to meet his five Central Asian counterparts and reassure them of continued US engagement in the strategic region.
On the fringes of that meeting, he spoke to Uzbek President Islam Karimov, who has ruled Uzbekistan for a quarter of a century and is often criticized internationally for heading a repressive government.
It was the highest-level US encounter with Karimov in years.
Most of the five former Soviet republics in Central Asia have poor human rights records, and a US official insisted that Kerry, on a four-day tour of the region, has not shied away from raising the issue "robustly" behind closed doors.
But he took pains to avoid direct public criticism as he pursued security and economic concerns at the top of his agenda.
"The United States does support the sovereignty and territorial integrity and independence of each country that's represented here," Kerry told the ministers' meeting.
That message has taken on greater importance as Washington draws down its forces in Afghanistan, concerns mount about the threat to the region from Islamic State, and Russia, fresh from forays into Ukraine and Syria, reasserts its influence.
It was Kerry's first meeting as secretary of state with Karimov, one of several former Soviet Communist Party bosses in the region whose grip on power has tightened over the years.
Kerry made no explicit mention of human rights when reporters were allowed briefly into the room at the start of the talks. But he said he wanted to discuss with Karimov and Central Asian foreign ministers "the human dimension, the issues of individuals and their participation in society".
As security men starting ushering reporters out of the room, one American reporter shouted a question to Karimov about the US State Department's own scathing critique of his human rights record. Karimov ignored the query. Kerry began responding but the reporter was pushed out of the room before he finished.
A later summary of the meeting by the State Department said the two men had talked about "respect for human rights and political freedoms" along with security and economic issues.
A senior US official said only that Karimov "took on board that he would look into it" and that real progress would require persistent US pressure.
At the foreign ministers' meeting, Kerry also appeared to soft-pedal human rights in his public comments.
But he advised the ministers of Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan and Uzbekistan that "in Central Asia as elsewhere, people have a deep hunger for governments that are accountable and effective."
Though none of the other ministers mentioned the issue in their statements, a joint final communique said the states were committed to protecting human rights and developing democratic institutions. But it offered no specific reforms or timetables.
They also declared support for Afghanistan's development as a "peaceful, thriving" state and an intention to counter cross-border threats such as terrorism.
International human rights bodies list Karimov's government as among the world's most repressive. The latest State Department global report on human rights cites torture, forced labour in the Uzbek cotton fields and "endemic corruption".
A US official said Kerry's aides raised with Uzbekistan's foreign minister some specific cases of political prisoners.
At the same time, however, the Obama administration is mindful of Uzbekistan's strategic importance. It has been, for example, a reliable partner providing logistical support for the US-led military campaign in neighbouring Afghanistan.
The renewed US focus on Central Asia coincides with warnings from Russian officials about the danger of Islamic State terrorists infiltrating the region from Afghanistan, accompanied by hints Moscow will respond by beefing up its military presence.