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Russia said on Saturday that the "unfounded accusations" of Austria in a spying scandal were unacceptable, the suspect having been placed in custody.
On Friday, Austrian Chancellor Sebastian Kurz said that an investigation had been opened on a colonel suspected of espionage on behalf of Russia for several decades.
The spying line is likely to harm Russia's ties with one of the few European allies.
This is the latest in a series of cases in which Moscow is accused of espionage in EU states and elsewhere.
Moscow said that Austrian Foreign Minister Karin Kneissl had called her Russian counterpart Sergei Lavrov to explain the reasons for Vienna.
She "expressed the hope that these measures will not affect the development of bilateral cooperation," said the Russian Foreign Ministry in a statement.
Lavrov reiterated Moscow's dissatisfaction that Austria has chosen to express its grievances in public.
He added that the practice of publicly expressing "baseless accusations" was unacceptable, said the Foreign Ministry.
"All possible mutual concerns must be discussed through established and evidence-based channels of dialogue," the statement said.
However, Kneissl said in a statement that during the appeal, she had defended the actions of Austria, which were "based on solid facts".
"The case concerns events that are punishable by law and required the intervention of prosecutors, which meant that it was inevitable to make the information public immediately," the statement said.
"We hope that the Russian authorities will cooperate fully to explain this case," Kneissl said, calling it "unacceptable interference in domestic affairs."
In August, Kneissl provoked a quarrel in Austria and beyond after waving with Russian President Vladimir Putin and bowing to him at his wedding. Critics claimed that his behavior undermined the country's image.
The 70-year-old suspect in the center of the line was taken into custody for interrogation on Saturday.
Austria suspects he has been working with Russian intelligence for several decades and has been investigating for revealing state secrets.
Colonel Michael Bauer Bauer, spokesman for the Austrian Ministry of Defense, told Kurier newspaper on Saturday that the information conveyed by the suspect "went from unimportant things to more sensitive information".
However, other media have hinted that Colonel was not able to reveal the highest levels of classified data.
The Salzburger Nachrichten newspaper reported suspicions that it had transmitted information from seminars and NATO courses it had attended, as well as information available on the army intranet system.
The newspaper says that he has also provided written portraits of various members of the military and his impressions of the atmosphere in the various departments of the army.
Austria is not a member of NATO and attaches much importance to its neutral country status.
It was one of the few European countries not to expel Russian diplomats after the poisoning of former spy Sergei Skripal and his daughter Yulia in Britain in March.
