US Secretary of State John Kerry met with Austrian Foreign Minister Sebastian Kurz before departing from Vienna on Tuesday, following a three day visit.

"Of course I have addressed the spy affair," Kurz told the Austrian Press Agency.

There were still some "unresolved issues", he said in reference to media reports that German spies had been operated by CIA agents based at the US embassy in Vienna.

He has agreed with Kerry and US ambassador Alexa Wesner that "the responsible persons will be available for experts from the ministry of the interior and the ministry of defence to clarify pending issues."

"Maybe the matter will be resolved, maybe it won't, and if so we will take appropriate action," Kurz added.

There have been allegations, raised by the German news magazine Der Spiegel, that a US spy who worked for German foreign intelligence (BND) has met at least two CIA agents working at the US embassy in Vienna several times since 2012.

The scandal has chilled German relations with Washington to levels not seen since Chancellor Angela Merkel's predecessor opposed the US invasion of Iraq in 2003.

It follows allegations that Merkel herself was among thousands of Germans whose mobile phones were bugged by American agents.

Kerry was in Austria to take part in nuclear negotiations with Iran. According to Kurz he thanked Austria for its "hospitality" and the opportunity to conduct negotiations in Vienna.