Delegates from about 180 countries are expected to attend the biennial conference of the WHO Framework Convention on Tobacco Control (FCTC) in India from November 7 to 12.
Pakistan's State Minister of Health Sciences Regulation and Coordination, Saira Afzal Tarar, said that Pakistan cannot attend the conference.
"It is an important meeting on tobacco. As far as Pakistan's participation is concerned, it is not feasible due to ongoing tensions," she said.
Friday's development came following a spat between the two countries after a staff member of Pakistan's High Commission in New Delhi was detained by police for questioning over espionage charges.
The tension intensified after tit-for-tat naming of diplomatic staff for alleged spy work by both sides. The latest incident further increased the tension that started with a militant attack on an Indian army camp in Uri in September.