The authenticity of the remains of the czar's family, slain by Bolsheviks in 1918 in the Russian Revolution, has been the subject of controversy for nearly a century.
"As a result of a probe, the Investigative Committee has come to the categorical conclusion that the remains are authentic," investigator Vladimir Solovyov said Thursday in Moscow.
The confirmation was based on "summarized data including court documents, genetic analysis, and historical and other materials," RIA Novosti quoted him as saying.
Nicholas II, his wife, their four daughters and son were shot to death in a cellar in the Urals city of Yekaterinburg in the early hours of July 17, 1918.
The remains of some of the family were discovered in 1991 and buried in the St. Peter and Paul Cathedral in St. Petersburg.
The remains of two of the children, Alexei and Maria, were discovered in 2007 near Yekaterinburg and confirmed by DNA tests.