The three men - a Turk, an Iraqi and a Syrian - were arrested in Istanbul on Tuesday by police acting on information from both Turkey's and Germany's intelligence services, Hurriyet newspaper and the broadcaster CNN-Turk reported.
The suspects, presented as members of an IS cell, are accused of plotting attacks on German interests in Turkey, the reports said.
Last Thursday, Germany closed its embassy in Ankara, its consulate in Istanbul and German schools in both cities, with Foreign Minister Frank-Walter Steinmeier citing "very serious" indications of planned attacks.
Turkish authorities had criticized the closures, saying they were unjustified.
Two days later, a Turkish alleged IS member blew himself up on a busy shopping street in Istanbul, killing three Israelis and an Iranian and injuring dozens.
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Tuesday's arrests in Istanbul come as police continue to hunt three Turkish suspected members of an IS cell believed to be planning further attacks in crowded public places.
A further 10 suspected IS members were captured Tuesday on Turkey's border with Syria, one of whom was wearing an explosives vest, officials said.
Two of those held in southern Gaziantep province were injured in an exchange of gunfire with Turkish troops. Three others managed to flee the scene, the local governor's office said.
IS has been blamed for four of six bombings that have rocked Turkey in the past eight months, including a massacre at a peace rally in the capital Ankara in October that claimed 103 lives and a bombing outside the Blue Mosque in Istanbul in January that killed 12 German tourists.
A radical offshoot of the rebel Kurdistan Workers Party (PKK), with which the state is embroiled in a bloody conflict in southeast Turkey, claimed the other two attacks.
SEE ALSO: Germany closes Ankara embassy 'due to terror threat'