Foreign Office in a statement said, "We condemn the detention and manhandling of our diplomatic official".
The Indian action has been accompanied by an "extremely negative and orchestrated media campaign", it said, adding the move "clearly reflects Indian actions to shrink diplomatic space for the working of Pakistan high commission".
"A staff member of the Pakistan high commission in New Delhi was lifted by the Indian authorities yesterday (26th October 2016) on false and unsubstantiated charges. He was, however, released in about three hours on intervention by our high commission," the statement said.
"We reject the Indian allegations and deplore the Indian action which is indeed a violation of the Vienna Convention as well as the norms of diplomatic conduct especially in an already vitiated atmosphere.
"Pakistan high commission has always been working within the parameters of international law and diplomatic norms," the statement claimed.
It also alleged that India's attempts to escalate the tensions and divert the international attention from the "grave human rights violations" being perpetrated in Kashmir can never succeed.
It urged the international community to "take notice of the Indian designs".
India's decision to declare a Pakistan high commission staffer in Delhi as persona non grata was conveyed by Foreign Secretary S Jaishankar who summoned Pakistan's envoy Abdul Basit.
Delhi Police crime branch took the staffer identified as Mehmood Akhtar in custody after he was found in possession of certain defence documents. Akhtar was released after questioning as he enjoys diplomatic immunity.
The crime branch has also arrested two persons, residents of Rajasthan, for allegedly passing on sensitive information to Akhtar..
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