Yildirim made the remarks at a Tuesday press conference, saying it is a “great mistake and greatly unfortunate” that Vienna made the decision shortly before taking over the presidency of the EU.
A spokesman for the Austrian government has declined to comment.
Last week, Austrian Chancellor Sebastian Kurz announced plans to order the closure of seven mosques and the expulsion of up to 60 imams, including 40 members of the Union of Turkish-Islamic Cultural Associations in Europe (ATIB).
The Federal Chancellor Sebastian Kurz also said the government was shutting down a Turkish nationalist mosque in the capital Vienna and dissolving a group called the Arab Religious Community that runs six other mosques, Presstv reported.
Kurz, who became chancellor in December in a coalition with the anti-migration Freedom Party, said the decision was made after an investigation into images of children, who were playing dead and reenacting the World War I battle of Gallipoli in Turkish-backed mosques.
He was referring to images, which emerged in April, showing children waving Turkish flags and then playing dead.
The Turkish-Islamic Cultural Associations (ATIB) organization denounced the photos at the time. It called the move as a "highly regrettable" event.
The Turkish government denounced Austria's decision to close mosques and expel imams as "a reflection of the Islamophobic, racist and discriminatory wave in this country."
Austria, however, is shutting down the mosques based on a 2015 tough “law on Islam” that among other things bans foreign funding of religious groups.
In a previous job as minister in charge of integration, Kurz oversaw the passing of the law.
The right-wing coalition government of Austria has been accused of fanning anti-Islamic sentiments in the European state. Austria is home to around 600,000 Muslims most of whom are Turkish or have families of Turkish origin.
The Austrian chancellor also insists that the European Union should cease negotiations about Ankara joining the bloc.
Irked by Kurz's stance, Turkey vetoed NATO's cooperation with Austria in May 2017.