"Such cooperation should not be to the detriment of Pakistan," Foreign Office spokesman Nafees Zakaria said in a statement.
The statement on the India-Afghanistan nexus comes two days after a report saying New Delhi will deliver more arms to Kabul to help it fight militants.
India has provided over $2 billion in economic assistance to Afghanistan in more than a decade.
New Delhi has also been assisting Kabul in building its war-ravaged buildings and heritage sites.
India assisted in building the Afghan Parliament complex as well as in restoring the Stor Palace in Kabul. These were jointly inaugurated by Prime Minister Narendra Modi and Afghan President Ashraf Ghani on December 25 last year and August 21 respectively.
New Delhi in December last year announced the supply of four military helicopters in India's first transfer of lethal equipments to Afghanistan since the hardline Taliban movement was toppled.
At a corps commanders' conference on August 9, top Pakistan army officers said the terrorist threat was transforming because of a growing nexus between hostile actors in the neighbourhood and facilitators within the country.
