A case of his disappearance and missing documents was registered at the Tarnol police station in Islamabad on a complaint of a defence ministry official, Dawn reported.
"It is suspected that he might have become a tool in the hands of enemy of the country," according to the FIR.
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He was given a sensitive assignment by the defence ministry, the paper said, citing the FIR.
He was made an official in-charge of some important and sensitive national affairs in Vienna, it stated, adding that "it was very important duty, besides sensitive for countrys sovereignty".
The official had been found absent from his duty since January 2, the FIR stated.
It said on checking of embassy's record the documents carrying sensitive information were also found missing.
After his disappearance, the man contacted his family and asked his wife to shift to her parents' house at Tarnol in Islamabad, the FIR stated.
According to his wife, her husband left the embassy of his free will and will "return after five years".
So far the man had not contacted his department or the Pakistani embassy in Vienna to inform them about his whereabouts, the FIR stated, adding that the wife, parents and brother of the man were in contact with him, but avoiding sharing information about him with the police.
In reply to a question, a police official on condition of anonymity said that the defence ministry had asked the law enforcement agency to investigate and interrogate his family to trace his whereabouts and arrest him.
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