Over the last two years prosecutors in Karlsruhe have dismissed 1,000 complaints of high treason against Merkel, the Mannheimer Morgen reported on Wednesday.
“The complaints against the Chancellor proved to have no basis to them,” said prosecution spokeswoman Frauke Köhle.
A large amount of the complaints came from supporters of the far-right Alternative for Germany (AfD) party, according to the report.
Federal prosecutors are responsible for following charges relating to the domestic and external security of Germany. They need to examine every individual complaint.
In September 2015 Merkel took the decision to take in refugees who had been camping in their thousands in Hungary. The decision eventually led to over a million asylum seekers arriving in Germany and proved extremely unpopular among some conservative voters.
The AfD argue that it was a breach of German asylum law, which stipulates that Germany does not have a duty to provide asylum to refugees which arrive in the country from other signatories of the Geneva convention. They accuse the Chancellor of threatening domestic security in Germany by allowing people to enter the country before checking their identities.
But the far-right party have also been accused of xenophobia after their leaders suggested during the refugee crisis that it was acceptable for border guards to shoot at people who cross Germany's border illegally, including women and children.
Merkel's refugee policy sent support for her conservative Christian Democratic Union party into a nosedive in 2015 and 2016 but her support has recovered as new arrivals have dwindled.
She now enjoys a double-digit lead in the polls against her Social Democratic rival Martin Schulz in her bid for a fourth term.
However, AfD supporters have been turning out in force to protest at many of her campaign rallies, particularly in the former communist east of the country.
In Bitterfeld-Wolfen late Tuesday, Merkel was met with a chorus of boos and cries of "get out!".
In a state election last year, the AfD scored around 32 percent of the vote in the city, once the heart of East Germany's chemicals industry.
At a later campaign event in the eastern city of Brandenburg an der Havel, the chancellor was also jeered, with some demonstrators holding signs saying "Merkel must go!", echoing a pro-democracy rallying cry in the late 1980s, "The (Berlin) Wall must go!".
The AfD, which groups extremist anti-Muslim and anti-migrant forces with more moderate voices, is currently polling at between eight and nine percent.