The main 80-meter-high dome of Trinity Cathedral, built in Russia's second biggest city in 1835, has collapsed. One of the cathedral's four smaller blue domes has also been consumed by the fire.
Hundreds of people have gathered round the cathedral, a major city landmark which recently underwent restoration.
An Emergency Situations Ministry Mi-8 helicopter was called in to tackle the flames, emergency services said earlier.
Icons and other valuable items are being evacuated and left outside the main entrance under police guard, he said.
No one has been hurt in the incident. Around thirty firefighting units are working at the site.
The first report of the fire came at 5:30 p.m. local time (13:30 GMT), emergency services said earlier.