The separatists, many of them ethnic Ingush allied to Chechens, killed almost 100 people and seized much of Ingushetia for several hours last Tuesday in their most audacious and successful raid for years.
"Magomed Yevloyev was eliminated in a special operation in Ingushetia this morning by our forces. He was on his own," Ilya Shabalkin, spokesman for the Russian military command in the North Caucasus, said on Monday.
Observers say the spread of war from Chechnya, where separatists have fought Russian rule of a decade, to other regions is a sign that President Vladimir Putin's policies are failing.
Putin refuses to negotiate with the separatists and says they are linked to "international terrorism". After the Ingushetia attack, he ordered the army to find and destroy the fighters.
Chechen officials say Yevloyev, an ethnic Ingush, was ordered to attack Ingushetia by separatist leaders Aslan Maskhadov and Shamil Basayev, who have led the fighters in Chechnya since war first broke out in the mountainous southern region in 1994.
Shabalkin said Yevloyev had fought in Chechnya but came to Ingushetia in December to spread the Chechen's campaign to the region, largely unscathed by fighting until this year.
"He was leader of the local Wahhabites," Shabalkin said, referring to local Muslims.
Separatist-linked news sources did not confirm or deny the report. News agencies quoted Russian prosecutors as saying 10 men had been detained after the attacks, and three charged.
Human rights groups say police have detained dozens of people, some in swoops on camps for Chechen refugees in Ingushetia.
Some estimates put the number of civilian lives lost in Chechnya at 70,000 since the first war of independence in 1994.