According to sources, the note verbale cited three specific incidents of Indian diplomats being harassed in Islamabad on Thursday.
The vehicle of the Indian Deputy High Commissioner, while he was going to an embassy within the Diplomatic Enclave for a meeting, was aggressively followed by two people in a Toyota Corolla car, the sources said.
The Indian Naval Attache was also aggressively followed by a person on a motorbike while going to Serena Hotel for a meeting.
In a third incident, the Second Secretary (Political) was "aggressively followed and harassed by a person at the Street-1 Cafe within the Diplomatic Enclave" while going there for an official meeting with another diplomat, a source said.
The website of the Indian High Commission continues to be blocked causing inconvenience and has affected normal functioning.
Last week, Pakistan called back its High Commissioner to India Sohail Mahmood for consultation over alleged harassment of its diplomatic staff and their families in New Delhi.
Following this, External Affairs Ministry spokesperson Raveesh Kumar during his weekly media briefing said that the Indian High Commission in Pakistan was facing "a litany of issues" which have not been resolved for several months.
"We raised these issues in good faith through diplomatic channels and not through the media.
"We have asked for immediate resolution of these issues faced by our High Commission in Islamabad so that the safety and security of the diplomatic mission and our diplomatic and consular officials is assured," he said.