"The relationship between Germany and Turkey is very broad and very deep," Steffen Seibert told journalists, underlining wide-ranging collaboration including on the migration crisis.
"Such ties can and will weather any differences in opinion," said the spokesman, who also pointed to the special relationship due to the three-million-strong ethnic Turkish population living in Germany.
Carrying a clear message from Merkel to any dissenting ethnic Turks in Germany, Seibert said: "You are and remain a part of our country".
The Bundestag or lower house of parliament yesterday overwhelmingly approved a resolution that describes the 1915-16 killings of Armenians by Ottoman forces as genocide.
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Ankara put up fierce opposition before and after the vote, recalling the Turkish envoy to Germany and summoning the German charge d'affaires in Ankara for consultations.
German lawmakers of Turkish origin came under particularly strong pressure over the vote.
Some had even received death threats in the run-up to yesterday's Bundestag session, said parliament speaker Norbert Lammert.