In Ankara on Monday, Merkel - referring to air strikes including those carried out by Russia - said "we are horrified in the face of this human suffering."
Her comments represented some of the sharpest criticism yet of Russia's aerial campaign by Merkel.
Russian President Vladimir Putin's spokesman said Merkel should carefully watch what she said on the Syrian crisis.
"We once again call on everyone to be very careful and responsible in their choice of words, given the already delicate situation in Syria now and the Syrian settlement," Kremlin spokesman Dmitry Peskov said.
Despite complaints from the West and the Syrian opposition, Russia had not received any credible evidence of civilian deaths from airstrikes, Peskov said.
He also said no voices had been raised in protest against the "barbaric actions of terrorists" when they assaulted Syrian regime forces in the past.
"No one made any statements of this kind at the time," Peskov told reporters.
Syria peace talks were suspended in Switzerland last week as the West and the Syrian opposition accused Moscow of targeting civilians and seeking a military solution to the nearly five-year war.
Asked on Monday whether Russia would press ahead with its bombing campaign in Syria if the peace talks resume, Peskov declined to comment.
Fears mount that Syria's mainstream opposition rebels risk total collapse after a Russian-backed regime advance that severed their main supply line to the city of Aleppo.
Relations between Russia and Germany have not been icy over the past few weeks, as Moscow blew up the alleged rape of a 13-year-old girl with dual Russian German citizenship into a diplomatic row.
In late January Russian foreign minister Sergei Lavrov accused Berlin police of covering up the girl's alleged abduction by migrants for reasons of political correctness, a move which Berlin described as “unacceptable.”
Moscow was widely seen as trying to incite fears about refugees among Germany's large Russian immigrant population in a strategic move to weaken an already fragile European consensus on the migrant crisis.
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Berlin prosecutors later showed that the girl had not been abducted but had spent the night at a friend's house.
Elements of the German media have been encouraging the government to take a tougher line on Moscow, with Germany's largest circulation newspaper Bild repeatedly saying that the Russian bombing in Syria is intended to worsen the refugee crisis in Germany.
International media meanwhile have suggested that Putin hopes to increase divisions in an EU that has placed painful sanctions on Russia since it annexed the Crimea from Ukraine in 2014.