Maksharip Aushev said he was replacing Magomed Yevloyev, a prominent journalist who was shot dead in a police vehicle, as the head of the www.ingushetiya.ru website and that a criminal case had been launched against him.
Following Yevloyev's death, which police said was caused when a gun accidently went off, thousands took to the streets in Ingushetia's main city Nazran. Opposition supporters have rejected the police version of Yevloyev's death.
In an emotional statement Aushev said Wednesday that a criminal case had also been opened against Magomed Khazbiyev, another opposition leader
"They are accused of disarming the Ingush interior minister's guards, who had detained Yevloyev at the airport," the statement said giving the names of the opposition journalist's alleged murderers.
A local Interior Ministry official said earlier Yevloyev had been detained by police at the local Magas Airport and was being driven in a police vehicle to Nazran for questioning regarding "a criminal case."
The website accused police in Ingushetia of persecuting those who took part in Monday's demonstrations rather than investigating the "cynical, blatant murder."
France's Foreign Ministry and the U.S. State Department have urged Russia to conduct a full investigation into the circumstances surrounding the journalist's death.
The Organization for Security and Cooperation in Europe (OSCE) said Yevloyev's death was an "orchestrated campaign by the authorities of Ingushetia to silence the only critical voice in the region," and "represents a further deterioration of media freedom in Russia."
Prosecutors are investigating the death as an involuntary killing.
The republic's Interior Ministry earlier said no clashes between police and protesters took place on Monday. It also denied some rights groups' reports that additional police reinforcements have been sent to Nazran.
Ingushetiya.ru was closed down earlier this year after being declared extremist. Local authorities said the website had called on people to take part in unsanctioned demonstrations in January. The protests against the local administration were banned over public safety fears. The decision to close the website was approved by a Moscow court in August.
In a separate incident Telman Alishayev, an anchor in a popular religious TV program Peace to Your Home, died on Wednesday after he was shot Tuesday night by gunmen in the south Russian republic of Daghestan, a police official said.
Russia remains one of the world's most dangerous countries for reporters. According to data from the international organization Reporters Without Borders, 21 journalists were murdered in Russia between 2000 and 2007.