MOSCOW — Ever since the remains of the last czar, Nicholas II, and most of his family were exhumed 25 years ago from a dirt road in the Urals, investigators, historians, and surviving members of the Romanov dynasty have anticipated the day when all the mur­-dered royals would be laid to rest.

They thought that moment had finally arrived when a funeral was scheduled last October for two long-lost children — Czarevitch Alexei and Grand Duchess Maria, whose remains were found in nearby woods many years later.

But it was not to be. The Russian Orthodox Church interceded, questioning whether any of the remains were authentic, and the service was postponed indefinitely. The nearly 100-year saga of murder, mystery, and myth lived on.

“The problem is that from the historical, scientific, and genetic point of view, it is absolutely clear that the remains of the czar and his family are authentic,’’ said Sergei V. Chapnin, who was fired as editor of The Journal of the Moscow Patriarchate in December, partly, he thinks, because he pushed for accepting the remains. “The only statement we hear from the church is, ‘We don’t believe it.’ ’’

Why the church rejects the evidence filling some 25 volumes is one enduring mystery at the center of the case. Senior church officials have never fully explained it.

“The church is interested no less than anyone else, and maybe even more than anyone else, to determine the truth in this complicated issue,’’ Vladimir R. Legoyda, a church spokesman, saidlate last year. “There are questions that still remain and serious ones. So far we just touched the tip of the iceberg.’’

In 2000, the church canonized the royal family, upping the ante for authenticating the remains and possibly imposing new funeral rites, in that the relics of saints must be preserved above ground.

Also last year, Bishop Tikhon, a shadowy, influential Orthodox figure rumored to be the spiritual guide for President Vladimir V. Putin, cast doubt on the authenticity of the bones by describing various untested theories, as did a historian endorsed by the church.

To take just one of the more outlandish claims, the bishop hinted that the grave of Nicholas’ father, Czar Alexander III, had been vandalized and his bones interred in place of his son.

That theory was quickly disproved. An excavation found Alexander III’s grave had remained undisturbed since his burial in 1894, said Sergei V. Mironenko, the head of the Russian State Archives.

Tikhon was not available for interviews. Patriarch Kirill, the head of the Russian Orthodox Church, said at a conference of bishops this month that Putin himself had consented to an open-ended inquiry.

Virtually every expert involved in the case agrees that investigators have pieced together a plausible explanation of what happened to the family, while the church has failed to produce an alternative.

Early in the morning of July 17, 1918, the czar, his wife, their five children, as well as their doctor, a cook, and two servants, were executed in the basement of a house in Yekaterinburg, in central Russia.

The executioners first dumped the corpses in a mine. During transport to a deeper mine, a truck became mired in mud, and the remains were buried on the Old Kaptikovskaya Road.

That main grave was discovered in 1979 by amateur sleuths, and the bodies were finally exhumed in 1991.

In 1998, in St. Petersburg, Nicholas II; his wife, Czarina Alexandra Feodorovna; daughters Olga, Tatiana, and Anastasia; and the four retainers killed with them were buried together in St. Peter and Paul Cathedral, where all the czars since Peter the Great lie. The church in December took custody of boxes believed to contain the partial remains of Alexei and Maria.

Rejecting the bones will anger some Orthodox adherents, particularly those outside Russia. Accepting them will incense a conservative domestic faction that believes the Soviet government somehow faked the burial.

“Either decision will cause a scandal, so they would like to postpone it,’’ Chapnin said.