The two girls are reported to have travelled to Syria from their homes in Vienna earlier this year.
"We received information just recently about two 15-year-old girls, of Bosnian origin, who left Austria, where they had been living in recent years; and everyone, the families and the intelligence services of the two countries, is looking for them.
Both were recruited by Islamic State. One was killed in the fighting in Syria, the other has disappeared," he said in the interview published on Monday on the Israeli internet portal ynetnews.com.
When the Austrian Press Association (APA) asked the Foreign Ministry for confirmation, they said that there has been no independent confirmation of this information. Furthermore, they said, these are not isolated cases, as other teenage girls have disappeared to Syria.
The two Viennese girls, Samra K. and Sabina S - whose parents are Bosnian refugees - disappeared in April after saying that they wanted to fight in Syria.
They are thought to have travelled to Ankara by plane, and then on into the southern Turkish region of Adana. After that, their tracks were lost, although some posts on social media networks surfaced claiming to be from the girls - but these have not been authenticated.
An Islamic preacher from Bosnia who is based in Vienna, Mirsad O., (known by the Islamic name Ebu Tejma), was allegedly responsible for the radicalization of the two young girls, brainwashing them into joining the jihad.
He has denied this, and has said that he plans to sue the Österreich and Heute newspapers for libel. Mirsad O. was arrested for his role in an alleged terrorist funding network based in Austria in November.