Interior Minister Kashkar Junushaliyev did not show up for work on Tuesday, a ministry spokesman said, saying that Kursan Asanov, an opposition politician and a former senior security official, had taken over as acting interior minister.
Police had been ordered to ensure citizens’ safety and prevent clashes and looting, the same spokesman said.
Trouble erupted on Monday after police used teargas and water cannon to disperse thousands of people demonstrating against the results of a parliamentary election on Sunday which they demanded be annulled.
Western observers said the election, which appeared to have handed most seats to two establishment parties supporting closer links between the former Soviet republic and Russia, had been marred by vote buying.
One of the parties was close to Jeenbekov, the president.
Police had broken up one protest late on Monday, but protesters later returned to Bishkek’s central square and broke into the White House, which houses both the president and parliament, local news websites Akipress and 24.kg reported.
Protesters then broke into the headquarters of the State Committee on National Security and freed former president Almazbek Atambayev, who was sentenced to a lengthy prison term this year on corruption charges after falling out with Jeenbekov, his successor.
Opposition groups took over several more buildings, including the mayor’s office, and appointed their own acting head of national security, acting prosecutor general and a commandant of Bishkek though it was unclear how much actual power they wielded.
Protesters also freed several former senior officials jailed under Jeenbekov, including ex-prime minister Sapar Isakov and Atambayev’s former chief of staff Farid Niyazov.
Several provincial governors have resigned, according to local media reports which said public rallies had begun on Tuesday in several provincial centres, most of them anti-government.
Jeenbekov’s supporters were gathering in the southern city of Osh, the same reports said, where his brother Asylbek Jeenbekov called for unity and order.