According to the minister, who took part in the conference together with State Secretary Boštjan Šefic, the EU's borders are porous and do not prevent entry to the people who are not eligible for international protection.
"The situation we are faced with today is a threat to the fundamental concepts of the EU, as migrants are allowed to enter the EU, travel around and pick a country where they want to request for international protection," the minister said.
This practice became known as asylum shopping and it must be prevented, she stressed.
The word asylum per se should not automatically open the door to the EU, according to Györkös Žnidar.
She believes the migration flow should be stopped at the external borders of the EU, so as to avoid situations, when migrants are first allowed to enter the EU and then in the event their request for asylum is denied the procedure of their return to their home country cannot be implemented.
Europe should remain open to those who need help, but the migration crisis has once again shown that national measures of individual countries do not suffice. Regional cooperation is imperative, she stressed.
In a comment to the migration situation, Foreign Minister Karl Erjavec said in Ljubljana today that many migrants were coming from North Africa and were not fleeing any hotspots. "All this points to organised crime. The EU will thus have to pay more attention to the fight against criminal organisations dealing with trafficking in human beings."
Györkös Žnidar pointed to another challenge the region is faced with at the conference, that of honouring commitments and law. "As a lawyer I find it unacceptable for a country not to obey international rules and the commitments it has made," she said in a reference to Croatia's rejecting of the border arbitration award.
The minister also expressed discontent with Austria's continued border checks on the internal Schengen border with Slovenia.
"Despite the many measures Slovenia has introduced to make sure that the safety of Austria or any other EU country is not at risk, Austria continues with the policy that significantly encroaches on the right of free movement of people, a key EU liberty."
Šefic met Austrian State Secretary Karoline Edtstadler on the sidelines of the conference to exchange information about migrant situation in both countries and the region.
The pair agreed that any positive changes can be achieved only through cooperation, the Interior Ministry said in a press release.