“Opposition is part of a democracy,” Merkel, sitting beside Erdogan, said to reporters on Thursday.
More than 100,000 Turkish public officials and civil servants, including around 28,000 teachers, have been dismissed or suspended since the coup attempt which killed at least 241 citizens and police.
Merkel urged Erdogan to preserve the division of powers, freedom of expression and diversity.
In January, the Turkish parliament approved a package of constitutional reforms that will see more power placed in the hands of the president. The reforms, if affirmed in April’s referendum, will found a presidential system in place of the current parliamentary one.
"It shouldn’t be seen as a lifting of the division of power, as feared by the opposition," Erdogan said, defending his country’s reforms.
Ankara and Berlin have not seen eye-to-eye on freedom of expression. Turkey denied press accreditations to German journalists, while criticizing German courts for what Turkey deems as too lenient of sentences for leaders of the Kurdistan Workers Party (PKK), which is a named terrorist organization in Turkey, the European Union and the United States.
Merkel also stated that the two countries should more closely cooperate in the fight against “every kind” of terror, as both nations have experienced recent terror attacks.
Erdogan took time out to correct Merkel’s previous use of the term “Islamist terror.”
“The term 'Islamist terror' severely upsets us Muslims. Such a term cannot be used; this is not true,” Anadolu Agency quoted Erdogan as saying.
The two leaders found common ground discussing developments in Syria, Iraq and the Aegean Sea, Erdogan said.
“We have discussed what we can do in the fight against terrorism,” Erdogan said. “International terrorism is not an issue that any single country can manage alone. There should be international cooperation. As two NATO allies, I believe our cooperation with Germany, which is also part of the [anti-ISIS] coalition forces, should continue just as we performed for Ukraine.”
Turkey shelters more than 3 million Syrian refugees. About 1.4 million refugees came to Germany since 2015.
Erdogan said they discussed cooperation in the fight against terrorism, the refugee crisis and possible mutual steps in Syria.
Prior to the meeting, the German Defence Ministry had said it had refused a request from Turkey to share reconnaissance images gathered by the German military as part of the global anti-ISIS coalition for fear that Ankara will use the information to target Kurds.
There were no immediate reports of Erdogan and Merkel addressing that issue.
