Koper police said the majority of the illegal migrants were from Pakistan (32), Iran (17) and Turkey (14), with the rest coming from Morocco, Syria, India, Afghanistan, Algeria, Iraq, Tunisia and Kuwait.
The majority, or 66, crossed the border in the area policed by Ilirska Bistrica police.
Eighty were sent back to Croatia, whereas the remaining five intend to ask for international protection in Slovenia.
Meanwhile, the Italian authorities returned to Slovenia 16 illegal migrants, the majority from Iraq and Iran, and Slovenia sent them further back along the Balkan migration route, to Croatia.
As part of border policing in the Koper area, police officers arrested a 30-year-old Bosnian citizen residing in Ljubljana who had transported 18 foreigners in a van. The investigating judge remanded him in custody.
They also apprehended a 40-year-old woman driver with Slovenian and Croatian citizenship and residing in Italy's Trieste, transporting four Indians, but the investigating judge released her.
The police also pulled over a van transporting eleven illegal migrants, but the driver fled and is still on the run.
The police in the south-eastern region of Dolenjska caught 72 foreigners who had entered Slovenia without required documents in various locations in the area.
The illegal migrants, citizens of Pakistan, Syria, Iran, Bangladesh, Algeria, Libya and Iran, are still being processed by the police.
The remaining two migrants, both from Pakistan, were found on a cargo train by Dobova border police and sent back to Croatia.
