From Strategy Page:
September 28, 2010: Recently Russian announced that, after an absence of nearly a century, chaplains were being reintroduced into the armed forces. This came after four years of negotiations with the Russian Orthodox Church, which would have to provide priests to be military chaplains. While the Orthodox church agreed, in the 1990s, to provide religious services to military personnel and their families, this did not include chaplains. That's because, despite the shortage of priests, it was possible to use lay people to provide some priestly functions (like counseling and organizing charitable activities). Chaplains, on the other hand, are typically assigned to military units, like other specialists (doctors and staff officers). There were not enough priests for that, because the communists had limited the number of men who could become priests during the Soviet period (1921-91). But the church worked out a compromise with the military, and chaplains will be phased in as priests become available.
Chaplains were eliminated in the early 1920s, when the Russian civil war ended, with the victory of the communists. The chaplains were then replaced with "political officers" (Zampolits), who served many of the same functions (looked after morale, and correct thinking). But the current move to bring back chaplains is part of an effort to stamp out the custom of older troops hazing and exploiting younger ones.
This hazing developed after World War II, when Russia deliberately avoided developing a professional NCO corps. They preferred to have officers take care of nearly all troop supervision. The NCOs that did exist were treated as slightly more reliable enlisted men, but given little real authority. Since officers did not live with the men, slack discipline in the barracks gave rise to the vicious hazing and exploitation of junior conscripts by the senior ones. This led to very low morale, and a lot of suicides, theft, sabotage and desertions. Long recognized as a problem, no solution ever worked. But getting rid of conscripts is believed to be a good first step. Volunteers will be in for more than two years, and Russia is developing professional NCOs to keep things under control in the barracks. However, it's been found that even among volunteers, the hazing tends to survive. While the new NCOs have had some success in suppressing the hazing, the generals don't want to take any chances. Thus the attempt to bring back chaplains.
There is, however, a problem. In the military, a third of the troops don't believe in religion at all, and nearly 20 percent of those who do are not Russian Orthodox. Meanwhile, the Russian Orthodox Church actively opposes other religions trying to get established in Russia. The government has gotten involved, passing laws that, in effect, outlaw some "foreign" religions. There's also hostility towards Roman Catholics. There aren't many of them, but the Russian Orthodox Church is still sparring with the Roman Catholics over a thousand year old dispute that split the Christian church into Roman and Orthodox branches. So there is fear that the Orthodox Church will want control over the new Chaplains Corps, and give short shrift to chaplains of other religions. There is also fear that a Chaplains Corps dominated by Russian Orthodox clergy could lead to trouble for troops who belong to other religions that the Russian Orthodox do not believe should be in Russia (like Pentecostals, Mormons and so on.) Under the new agreement, all these potential problems are to be solved, somehow, in the future.