The shooting happened at about 7 a.m. at the Cathedral of the Resurrection in Yuzhno-Sakhalinsk on Sakhalin Island, RIA Novosti reported.
The gunman fatally shot a nun and a worshiper. A church spokesman said the six injured were hospitalized with non life-threatening injuries.
The attacker was taken into custody by police at the scene, authorities said. He was described as being in his 20s and a guard at a local agency. A motive for the shooting was not immediately known.