Yildirim paid an official visit to the capital Sarajevo on Thursday and Friday, Anadolu Agency reported.
Speaking to reporters, he said: "FETO is an issue for the entire world. The Balkan countries and in particular Bosnia and Herzegovina should not show negligence. The biggest danger is negligence."
Yildirim said that Turkey does not want its friends to experience the sufferings it went through during the failed coup attempt.
"You are wrong if you think: 'They are not doing anything. They have schools, they educate people, they deal with trade, they benefit people, they talk about press, publication, Islam.'
"We have seen their true faces. It is not like that. Turkey has experienced it. Because their minds are not their own minds. These are just like a spy agency of certain imperial powers.
"They work as imposters. How do they hide? They use Islamic values, enter your community, live like you, behave like you, but they are governed by someone else.
"Do you kill a Muslim person? Would you kill an innocent?..... We've experienced this. We don't want our friends to experience it," said Yildirim.
There are several FETO-linked educational institutes in Bosnia and Herzegovina. They include, four preschools, five elementary schools, five high schools, and a university operating in Sarajevo, Mostar, Bihac, Zenica, and Tuzla.
The International Burch University has played key role in structuring the network. Books spreading propaganda of the terror group have been published in the Bosnian language by Hikmet Publications.
FETO and its US-based leader Fetullah Gulen orchestrated the coup attempt on July 15, 2016 that martyred 250 people and left nearly 2,200 injured.
Ankara also accuses the group of a long-running campaign to overthrow the state through the infiltration of Turkish institutions, particularly the military, police, and judiciary.
Yildirim also met several media representatives of the country.