Faymann will meet Croatian Prime Minister Zoran Milanovic in Zagreb at 8am after which he will travel to Ljubljana to meet Slovenian premier Miro Cerar at 11am, his spokeswoman said.
Hungary this week sealed its southern border with Serbia, cutting off one of the biggest entry points for migrants into the European Union , prompting several hundred migrants to enter Croatia on Wednesday.
Milanovic has said the migrants will be given free passage to wherever they wish to go, meaning they will likely pass through to Slovenia, which borders Austria, Italy and Hungary.
Preparing for the possible arrival of thousands of people through its border with Slovenia, Interior Minister Johanna Mikl-Leitner said on Tuesday that Austria would introduce border controls along its southern frontier.