MOSCOW — The Ukrainian authorities halted all trade with two Russian-controlled separatist enclaves in the country’s east on Wednesday, using an economic weapon to strike at what has been a long-festering military problem.

The decision to block all but humanitarian trade dealt another blow to the much-beleaguered Minsk peace process and raised tensions not just with the separatists but with their patrons in Moscow, who could be called upon to provide aid and markets to the breakaway regions.

President Petro O. Poroshenko has been reluctant to isolate the breakaway areas, in a region known as the Donbas, fearing that would implicitly recognize their independence and be a first step toward the country’s partition.

But the idea of halting trade has long animated Ukrainian nationalists as a way to shift the cost of sustaining the approximately three million people in the eastern region onto Russia’s already weakened economy. In recent weeks armed bands of men in tattered camouflage had begun doing exactly that, blockading rail shipments from the east, mostly coal trains.