Confirming press reports, a Nato official said: "We regret the current situation and the impact it is having on all of our cooperation programmes with partners."
"Nato supports constructive dialogue between countries. We count on our ally Turkey and our partner Austria to solve their bilateral issue swiftly," the official said.
Austrian Defence Ministry spokesman Stefan Hirsch confirmed to AFP that the "Turkish blockade of Austria's partner programmes with Nato began several months ago".
"It has no immediate impact on our missions in the western Balkans. But in the mid- to long-term, the blockade can lead to problems because it can hinder our ability to prepare new missions," he said.
German daily Die Welt said the Turkish action effectively blocked all of Nato's various cooperation programmes with non-member states.
These programmes cover most of Europe, plus many countries in the Middle East and Asia, and are aimed at building up inter-operability, capacity and goodwill.
They do not involve the Nato collective defence commitment for member states but are seen as an important political signal, for example in partner countries such as Georgia and Ukraine locked in bitter disputes with Soviet-era master Russia.
Hirsch added that diplomatic talks with Ankara were ongoing and that Austria, as one of the biggest providers of troops in Kosovo, was counting on Nato to help find a solution.
Turkey restarted European Union accession talks in 2005 but they have made painfully slow progress amid growing questions in Brussels over its human rights record.
Relations have soured badly since a failed military coup in July against President Recep Tayyip Erdogan, who embarked on a widespread crackdown in response and is now seeking increased powers in a referendum next month.
Austria, a member of the European Union but only a so-called partner country for Nato, has repeatedly called for the EU accession talks to be frozen.
The EU in December said it would open no new areas in the talks, but Austria refused to sign the statement because it wanted all current negotiations to be completely halted.
Press reports said Turkey, the second largest military power in Nato after the United States, had retaliated by suspending cooperation with the partner countries of the alliance.