Presidential spokesman Ibrahim Kalin said Europe was seeking to "whitewash" Gulen's group, while Defence Minister Fikri Isik said the comments raised questions about whether Berlin itself was involved in the putsch.
"How can terrorist organization be allowed to gather in Germany, while government ministers of the Republic of Turkey are not allowed to meet with our citizens?" he asked at a rally in the southern Osmaniye province's Kadirli district.
"It is impossible to explain for German authorities to claim that Turkey's elected representatives' meeting with their citizens is risky, but to treat terrorists as legitimate actors", Kalin added.
About 1.4 million Turks in Germany can vote in the April referendum.
Kahl also said he did not think the Turkish government was behind the coup, saying: "The coup attempt was not initiated by the government".
On the same day that PKK followers marched in Frankfurt, the deputy chair of Turkish ruling Justice and Development Party was banned from addressing local Turkish community in the northern German state of Lower Saxony. His comments came after the head of Germany's foreign intelligence agency, Bruno Kahl, said Ankara had failed to provide evidence of Gulen's involvement in the July plot.
He told German news magazine, Der Spiegel: "Turkey has tried to convince us of that at every level but so far it has not succeeded".
About 300 people, vast majority of them civilians, were killed after rebel soldiers attempted to overthrow the government on July 15, bombing state buildings and killing civilians and security forces.
The group is listed as a terror organisation not just by Turkey but also by the European Union and the United States.
Turkey's foreign ministry expressed its displeasure to Germany's ambassador in Ankara, according to a statement by the ministry.
"It's an effort to invalidate all the information we have given them on FETO".
Tensions are already running high between Berlin and Ankara after German authorities refused to allow some Turkish ministers to campaign in the country for a "yes" vote ahead of the April 16 referendum on handing Erdogan an executive presidency.
Tens of thousands of people were arrested and civil servants were sacked in the purges after the coup attempt.
The constitutional change would give Erdogan sweeping new powers.