Erdogan has angrily condemned last week's vote on the World War I massacres, charging that the 11 German MPs with Turkish roots who backed it supported "terrorism" by the banned Kurdish Workers' Party (PKK), and demanding "blood tests" to see "what kind of Turks they are".
Merkel's spokesman Steffen Seibert on Monday said that while Berlin also considers the PKK a terrorist group, "to associate individual members of parliament with terrorism is utterly incomprehensible to us".
"The resolution was a political initiative that emerged from the midst of the Bundestag, which is a democratically elected, independent organ under our constitution," Seibert told a regular press conference.
"The Bundestag reached a sovereign decision. That must be respected," Seibert said, adding that this was the message Merkel had given to the Turkish president.
Erdogan -- in a bitter reaction to the vote to recognise the 1915-1916 killings as genocide -- singled out German Greens party co-leader Cem Özdemir, one of the instigators of the resolution passed on June 2.
Özdemir has been placed under police protection after receiving anonymous death threats.
The vote in the German parliament added yet another bone of contention to Turkey's troubled relationship with the European Union, and comes as the 28-nation bloc is banking on Turkey to block the flow of migrants into Europe.
The Turkish community in Germany -- which broadly opposes the 'genocide' vote -- nonetheless criticised Erdogan Monday for the pressure his government and its supporters had placed on German lawmakers of Turkish origin.
"We find death threats and demands for blood tests abhorrent," its chairman Gokay Sofuoglu told national news agency DPA.
"I think the era when people were defined by their blood ended in 1945.
This is absolutely out of place."