The two Indian diplomats, who were at the gurdwara to facilitate Indian pilgrims, were also threatened and asked never come to the area again.
India has raised its concerns with Pakistan over harassment of two of its diplomats by intelligence personnel last month and asked it to conduct an inquiry and prevent recurrence of such incidents, sources said in New Delhi on Saturday.
It also conveyed its concerns regarding security of the Indian High Commission in Islamabad.
The two Indian diplomats, who were at the gurdwara to facilitate Indian pilgrims, were also threatened and asked never come to the area again.
They were locked up in a room by about 15 Pakistani intelligence personnel, their bags were searched and they were questioned.
India had earlier this year also raised concern over harassment of its diplomats with Pakistan.