I do not have access to NKVD files, whatever they say, but the story is well documented in the literature, including the Russian literature (memoirs of Russian soldiers).
One especially good source is memoirs of Lev Kopelev, a Russian author, who tried to protest and was imprisoned for his protests (see Wikipedia).
There are many other memoirs of Russian soldiers.
NKVD did try to fight this, at least on some later stage, and certain number
of Soviet soldiers were tried and punished for rape, violence, robbery and murders.
However the number trials was too small in comparison with the enormous scale of rape and violence
that actually occurred.
The victims of rape were not only Germans but also foreigners of all nations, people displaced by war for various reasons, including camp inmates. Same happened not only on the enemy territory but
also on the territory of the allies, like Yugoslavia. On Yugoslavia, the best source is the memoirs of Milovan Djilas (Memoir of a Revolutionary, 1973,
who was a top communist Yugoslav politician at that time.
Unfortunately, all references that I now have are in Russian, including Djilas.
But there exist also many German ones, including two German movies, based on published accounts of the victims, that I have seen.
This Wikipedia artile gives a survey of the subject and some English references:
You also ask about Soviet leadership. There is no doubt that leadership knew what is going on. It also tried to restrict violence but too late and too little. All memoirs agree in that the violence was strongest in the beginning of
occupation of Germany, that some high commanders considered it normal and justified it, and official media encouraged it (I. Ehrenburg's articles in central newspapers, for example). At a later stage they tried to restrict it, probably out of concern about discipline of their army.