Addressing the press two days after around 3,000 people gathered in Šenčur near the city of Kranj to protest against plans for a refugee shelter, he said "there is no reasonable basis for fear".
Cerar said that certain political players would favour disorder and chaos in order to be able to come to power.
He said Slovenia was not about pitting people against each other and that the spirit of the Constitution called for tolerance and readiness to help people.
Cerar argued people are being unconstitutionally turned "against something that does not exist" and that those doing this are doing it for reasons that do not benefit Slovenia.
Almost half a million people have passed through Slovenia since October and things remained under control all along, he stressed.
"We successfully protected people, property, public peace and order and we plan to continue to do so."
Cerar explained that presently accommodation facilities were being sought for migrants who need to be helped and subjected to certain procedure before they continue their path. Any migrants to potentially cause incidents at these facilities would be immediately removed, he added.
As regards the international situation, he said his initiative for tighter controls on the Greek-Macedonia border has been acknowledged and supported by a great majority of the players. He added that this was the only migrants-related initiative that will really begin to be implemented.
The prime minister's statements came as a stricter regime is being put in place on "the Balkan refugee route" and after Saturday's protest in Šenčur, which also featured some of the MPs of the opposition Democrats (SDS) and New Slovenia (NSi).