The decision was announced by PM Miro Cerar after being taken by the government at a session held as part of its two-day visit to the north-eastern region of Pomurje.
Cerar said the measure was meant to better control the movement of people and so the authorities were not caught unawares in the event of a large group of refugees entering the country.
"These things need to be kept under control so as to avoid any instability," Cerar said, assuring the public the government was prepared for a variety of probable scenarios.
Interior Minister Vesna Györkös Žnidar, addressing a special news conference dedicated to the issue in Ljubljana, described the measure as "unavoidable and needed" to manage migration flows.
She said the measure was needed so that persons coming to Slovenia got decent treatment and to ease the work of police officers processing them as well as avoid any threat to public order and internal security.
The measure was proposed by the Interior Ministry so as to ensure a gradual passage of refugees as the accommodation facilities that are being prepared by the country are made available.
The ministry had so far collected information on the possible facilities for the accommodation of more than 2,000 people with the help of local authorities and private individuals.
After Hungary closed its border with Serbia, it is increasingly likely refugee routes would be diverted, also through Croatia and Slovenia.
Croatia has estimated about 4,000 refugees will enter the country in the coming days. Only today close to 900 refugees reached the country by the evening.
The crisis was discussed by the Slovenian and Croatian home ministers with Croatia's Ranko Ostojić telling parliament in Zagreb they discussed the possibility of establishing special corridors for the transport of refugees.
This was denied by Györkös Žnidar. She said such corridors would contravene with the national and the EU legislation.
Cerar too said the country would respect the Schengen regime on the border with Croatia and act in accordance with national and EU legislation in the case of arrival of migrants and refugees.
"We mustn't fear that in Slovenia. We must manage the situation, help people in need, while treating them in line with the prescribed procedures and taking into account integration and security aspects."
This is the first time since the country joined the Schengen passport control-free area in 2007 that Slovenia will apply a temporary suspension of the regime.
The European Commission confirmed it had been notified of the measure, but could not yet comment because it was still examining it.
Meanwhile, concern was expressed by Slovenian MEP Tanja Fajon (S&D/SD), while Milan Zver (EPP/SDS) expressed fear about the country's absorption capacity, urging solidarity at the EU level.
The Chamber of Commerce and Industry's (GZS) Transport Association meanwhile warned of potential costs reinstated border controls would cause to the haulage industry.
Similar steps have already been taken by Germany and Austria. Austrian police also started checks in the evening at three major crossings with Slovenia, Šentilj, Karavanke and Ljubelj.
Cerar is due to meet over the crisis his Austrian counterpart Werner Faymann in Ljubljana tomorrow, after Faymann is to hold talks on the matter in Croatia.