Police then pushed the demonstrators back, tearing down banners and knocking at least one protester off their feet, the Reuters news agency reported.
Ban is on a tour of Central Asia and is being closely watched for how strongly he pushes human rights issues in a region that, activists say, is being run by authoritarian leaders who tolerate little dissent.
"We want Ban Ki-moon to start paying attention to what is happening here, to the fact that human rights are being violated here and that Kyrgyzstan uses repression against its own people," Asiya Sasykbayeva, a human rights activist, said.
"There is no media freedom in this country. There is no alternative information. Dissent is being suppressed."
Ban later called on Kyrgyzstan to do more to protect human rights.
"Quite frankly, recent events have been troubling, including the last few days," he said.
"I repeat: all human rights must be protected, including free speech and freedom of the media"
"I repeat: all human rights must be protected, including free speech and freedom of the media."
The Kyrgyz authorities have recently cracked down on independent media, seizing equipment in a raid on a television station, effectively taking it off the air, and closing down an opposition newspaper.
In March, the courts banned two newspapers close to the Kyrgyz opposition and fined them $111,000 for having attacked the honour of Kurmanbek Bakiyev, the Kyrgyz president.
Two prominent journalists were killed in the region late last year and several independent media websites and radio stations have not been accessible in Kyrgyzstan since early March.
Ban arrived in Kyrgyzstan as part of an official tour of Central Asia that also takes in Kazakhstan, Tajikistan, Turkmenistan and Uzbekistan.
Advocacy groups have accused the West of putting oil and security above democracy in its contacts with Central Asia, a region lying on vast energy reserves and serving as a transit route for supplies headed for Nato troops in Afghanistan.
"We are deeply disturbed by the actions of Kyrgyz authorities to systematically unplug their citizens from independent and opposition news sources," the US-based Committee to Protect Journalists, said in a statement.