Foreign Minister Sergei Lavrov said the adoption of the legislation by Ukraine's parliament "in essence rewrites the agreements or, more simply put, grossly violates them" despite Kiev arguing it is in line with the February peace pact.
He objected to Kiev's requirement that before autonomy is granted, the separatists must hold local elections under Ukrainian law, with international monitoring.
Lavrov said this made the "liberation of the territories that they say are occupied" a prerequisite of the law.
"Only when these territories are headed by people suitable for Kiev will the law come into force."
Ukraine's Verkhovna Rada parliament on Tuesday adopted the two bills enshrining greater autonomy for areas controlled by pro-Russian rebels, despite fierce criticism from separatists and nationalists in Kiev.
The passing of the legislation was a key plank in a peace deal signed by Kiev and the rebels last month after marathon talks between the leaders of Ukraine, Russia, Germany and France in the Belarusian capital Minsk.
The areas to be given a form of self-rule -- including greater status for the Russian language -- are listed for the first time in the texts adopted Tuesday, which also set out conditions for the changes to take effect.
The dispute over the latest step in the painstakingly-negotiated deal threatens to derail the peace plan just as a lull in conflict raised hopes of an end to over 11 months of bloodshed that has left more than 6,000 people dead in eastern Ukraine.
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