Interior Minister Arsen Avakov said about 70 "separatists" were arrested.
Writing on his Facebook page, Avakov said the city center had been sealed off but that the subway was in operation.
Ukraine's Interior Ministry was quoted by Interfax-Ukraine news agency as saying those detained were suspected of "illegal activity related to separatism, the organization of mass disorder, damage to human health" and breaking other laws.
After news of the operation early on April 8, Russia's Foreign Ministry called on Kyiv's authorities to stop massing military forces it claims are intent on suppressing anti-government protests in southeastern Ukraine.
"According to our information, units of the Interior troops and Ukraine’s national guards as well as militants from the illegal armed formation ‘Right Sector’ are being amassed in the southeastern parts of Ukraine and in the city of Donetsk,” the ministry said, according to ITAR-TASS.
It suggested U.S. mercenaries were involved. "We are particularly concerned that the operation involves some 150 American mercenaries from a private company Greystone Ltd., dressed in the uniform of the [Ukrainian] special task police unit Sokol," the ministry said.
Russia on April 7 warned authorities in Kyiv against using force against pro-Russian crowds.
WATCH: In Donetsk, pro-Russian protesters remained in control of the regional administration building on April 8.
Pro-Russian protesters seized government buildings in the eastern cities of Kharkiv, Luhansk, and Donetsk on April 6, demanding that referendums be held on whether to join Russia.
Acting President Oleksandr Turchynov told Ukrainians in a televised address on April 7 that "a second wave of the Russian Federation's special operation against Ukraine [has] started" with the "goal of destabilizing the situation in the country, toppling Ukrainian authorities, disrupting the elections, and tearing our country apart. "
He described those who had seized the administrative buildings in eastern Ukraine as "separatist groups, coordinated by Russian intelligence services," adding, "And what is most dangerous: They took up weapons."