The former agent with the BVT domestic intelligence agency is accused of illegally accessing classified information between 2015 and 2020, according to documents seen by the Die Presse newspaper.
He is then alleged to have sold the secrets to Russia and to Austrian politicians.
“He is in detention,” Christina Salzborn, the vice-president of Vienna's regional criminal court, told AFP, without giving further details.
He is also accused of passing information to a senior executive of Wirecard, an online payments firm that collapsed in June after it was forced to admit 1.9 billion euros ($2.2 billion) missing from its accounts did not exist.
The executive, Jan Marsalek, is on the run and features on Interpol's most wanted list.
Austria makes much of its neutral status and attempts to foster good relations with Russia.
But the allegation of leaks at the BVT is the latest in a series of embarrassing scandals casting doubt on Austria's reliability on security matters. In June, a retired Austrian army colonel was jailed for three years after being convicted of spying for Russia.
In 2018, Western intelligence agencies reportedly limited cooperation with Austrian partners after Herbert Kickl of the far-right Freedom Party (FPOe) was installed as interior minister.
The FPOe has a partnership agreement with Vladimir Putin's United Russia party.
Kickl sparked controversy early in his term by ordering a raid on the BVT's headquarters during which numerous sensitive documents were seized.
His time in office ended when the coalition between the FPOe and the centre-right People's Party collapsed in scandal in May 2019.