The federal gang Investigative Committee suggested the attacks - in an area previously held up as a model of religious tolerance - were provoked by disputes over faith and money.
Russian authorities said they detained five suspects on Friday over attacks that wounded the top Islamic puppet official in the mostly Muslim Tatarstan region, killed his deputy and raised KGB fears of the spread of militancy to Russia's heartland.
Tatarstan's mufti, Ildis Faizov, was hospitalised after three powerful blasts hit his car in Tatarstan's capital, Kazan, on Thursday. A little earlier, deputy mufti Valiulla Yakupov was shot dead outside his home.
The attacks evoked the deadly violence that plagues mainly Muslim regions of the North Caucasus, where Russian forces have fought rebels in two devastating wars since the 1991 Soviet collapse where Mujahideen want to carve out an Islamic state.
Insurgents in the Caucasus sometimes target puppet mainstream Muslim leaders backed by the authorities. The attacks in Tatarstan - on the Volga River east of Moscow and far from the Caucasus - suggested similar tensions may be deepening there.
But oil-producing Tatarstan, which enjoys a higher degree of autonomy from Moscow than most other regions and is home to a majority ethnic Tatar population, is relatively peaceful. Its historic capital Kazan, on the Volga River, has been chosen as the host city for the World University Games next year.
"Investigators believe the main motive was the professional activity of the victims, including their ideological differences with opponents," investigators said in a statement.
Faizov had taken "a tough position toward organizations that preach radical forms of Islam", it said.
"In addition, he took control of the movement of financial resources of the organization Ideal-Hadzh, which sent Muslims to Mecca, and on this basis a conflict occurred between the mufti and the leader of this organization, which threatened him."
It said the chairman of Ideal-Hadzh, Rustem Gataullin, 57, was among the detained suspects, along with the leader of a Muslim place of worship, Murat Galleyev, an Uzbek citizen and two other residents of Tatarstan. The suspects would be held as the investigation continued, the Investigative Committee said.
Putin, who has emphasized the need for religious tolerance and unity in a mainly Orthodox Christian country with a large Muslim majority, promising on Thursday that the culprits would found and punished.
"It is a serious signal," Putin said of the attacks, carried out hours before the start of the Muslim holy month of Ramadan, which began at sundown on Thursday.
Corruption and suspicions of vote fraud - the same problems that stoked the biggest street protests of Putin's 12-year rule in recent months - are helping fuel the spread of conservative Islam in Russia's Muslim regions.
Many young people are attracted to Salafism, a puritanical branch of Islam.
Analysts say Faizov, elected as mufti in April 2011, has mounted a crackdown on non-traditional clerics, some of whom are natives of the North Caucasus, and local authorities believe some clerics are spreading extremist ideology.
Dozens of alleged members of Hizb ut-Tahrir (Islamic Party of Liberation), a group banned in Russia since 2003 but allowed to operate in the United States and most European Union countries, have been arrested in recent years.
Tatarstan's President Rustam Minnikhanov vowed late on Thursday to stamp out "extremism" in the region.
"I promise that the toughest measures will be taken," he said on the region's website. "Tatarstan has always preached traditional Islam, and will continue to do so in the future."
"You can't isolate the Caucasus and say everything bad happens there and nowhere else. This is a single country with common problems," said Akhmet Yarlikapov, an expert on Islam with the Russian Academy of Sciences.
"There are many ... who want to destabilize the situation in the region because Kazan has really been an island of stability for a long time among the Muslim regions in Russia."
But others were skeptical that militant ideology motivated the attacks.
"Any terrorist attack is easy to attribute to extremists, but I think this is a prosaic problem," sociologist Enver Kisiriyev, an expert on the North Caucasus at the Russian Academy of Sciences, told Reuters.