On Sunday, "four High Commission of India officials travelling in an official vehicle were aggressively followed by two unknown persons on motorbikes in an intimidating manner", the person cited above said.
Diplomatic sources mentioned that Pakistan has scheduled the WTO ministerial meeting to be held here from March 19-20.
Indian diplomats based in Pakistan have alleged that Pakistani intelligence officials have entered their residential complexes.
Sunday's note of protest is the 13th that Delhi has sent this year to Pakistan over harassment of its staffers and diplomats based at the High Commission in the Pakistani capital.
While India has said it is looking into the incidents, it sought to downplay them and stated that the visit of High Commissioner Mahmood to Islamabad is "routine and normal", according to Raveesh Kumar, Spokesperson, Ministry of External Affairs (MEA).
The officials rejected the allegations that Indian diplomatic staff was also facing obstacles and harassment in Pakistan.
The WTO meeting will be attended by the Trade ministers of over 50 nations including the USA and China among others where they will discuss issues related to agriculture and services.
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The decision to pull out of WTO meeting comes on the heels of recalling of Pakistan's High Commissioner to India Sohail Mehmood.
Spokesman to the Foreign Office (FO) Dr. Muhammad Faisal Friday said there was unprecedented increase in Indian violations at Line of Control (LoC) and working boundary.
On Saturday, the Indian High Commission in Islamabad had sent yet another complaint of harassment to the Ministry of Foreign Affairs of Pakistan.
India had also invited Pakistan to participate in the meeting which was confirmed by Pakistan's Commerce Minister Pervaiz Malik earlier in February. Reports in Pakistan suggested that the officials is unlikely to return soon to India.
In other words, Pakistan recalled its envoy to New Delhi as a protest till the situation improves.
India for its part has alleged that several Indian mission staffers in Islamabad have been severely "harassed and intimidated".