"The firing by separatists on Ukrainian troops who were withdrawing constitutes a serious breach of the ceasefire," he was quoted as saying.
International monitors said earlier Friday the conflict in Ukraine was at a "crossroads" as further losses among government forces rattle the two-week-old truce just as it had seemed to be gaining traction.
The deaths of the three Ukrainian soldiers came after a two-day lull in clashes with the pro-Russian separatists and highlighted the fragility of the ceasefire.
Ukrainian military spokesman Andriy Lysenko said the fighting had halted along most of the frontline but there were still clashes in villages around the ruins of Donetsk airport, one of the most fought-over prizes in the conflict, which fell to the rebels last month.
The latest skirmishes came as the UN geared up to discuss the conflict exactly one year after Russia began seizing ports and cities on the Black Sea peninsula of Crimea.
Russia's annexation of the peninsula from Ukraine sparked the worst East-West standoff since the Cold War.
A year on, the West is hoping the UN-backed truce deal negotiated by Russia, Ukraine, Germany and France in Minsk earlier this month can prevent a further escalation.
Poroshenko also brought Merkel up to date with the Ukrainians forces' implementation of the ceasefire deal, including the early withdrawal of heavy weapons" under the auspices of the Organization for Security and control cooperation in Europe (OSCE).
Merkel, without commenting on the latest clashes, insisted "on the need to put into effect all the measures agreed in Minsk," her office said.
She recalled Moscow's "responsibility" in the matter, urging it to pressure the separatists to adhere to the peace process.
The European Union, United States and Ukraine accuse Russia of being behind the rebels while Moscow denies directly supporting them.
Turkish diplomat Ertugrul Apakan, who heads the OSCE monitoring team, on Friday described rebel fighting around the town of Debaltseve in the days that followed the ceasefire deal as a clear violation of the Minsk accord.
Apakan asked the United Nations to help bolster his mission's capacity to monitor the truce by providing more access to satellite imagery, drones and image-gathering technology.
The Security Council was holding its first meeting since it endorsed the ceasefire deal reached in Minsk between Russian President Vladimir Putin and the leaders of Ukraine, France and Germany.