The main dome of Trinity Cathedral, built in Russia's second biggest city in 1835, collapsed earlier. The second dome to catch fire is one of four smaller domes.
"Fire fighters are trying to protect the remaining three small domes, as well as a part of the roof," the source said.
An Emergency Situations Ministry Mi-8 helicopter has been called in to tackle the flames, but the fire has not yet been localized, emergency services said.
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.