Speaking ahead of a trip to Damascus, outgoing foreign minister Annalena Baerbock said the violence had undermined faith in the Syrian authorities.
"Lots of them (Syrians) are scared that life in the future Syria will not be safe for all Syrians," Baerbock said in a statement.
"The appalling bouts of violence two weeks ago have cost a massive amount of trust."
Baerbock called for Syria's transitional government, which took office after former president Bashar al-Assad fled the country in December, to ensure it controlled the "groups in its own ranks".
She added that it should put those responsible for the violence on trial and ensure peace and prosperity across Syria, which has been scarred by 14 years of civil war.
"This is the mammoth task facing the Syria's transitional government under Ahmed al-Sharaa," she said.
In the days after March 6, Syria's Mediterranean coast was gripped by the worst wave of violence since Assad's overthrow.
According to the Syrian Observatory for Human Rights, security forces and allied groups killed at least 1,500 civilians, most of them Alawites, the same minority to which former president Assad belongs.
Baerbock said she would use her trip to tell Syria's government that a "fresh start" between Europe and Germany on one side and Syria on the other was conditional on all Syrians enjoying freedom and security regardless of faith, gender or ethnicity.
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