Defence Ministry sources said no official reason has been given by Pakistan for skipping the conference in New Delhi.
"An invitation was sent to Pakistan as well as all other countries of the SCO. Pakistan never responded to this invitation," a senior ministry official told IANS.
Pakistan has skipped the conference even as it is participating in a joint anti-terror military drill under the SCO that is simultaneously underway in Russia's Orenburg. The 15-day-long military exercise began earlier this week.
Apart from India and Pakistan and host country Russia, China and four Central Asian nations of Kazakhstan, Kyrgyzstan, Uzbekistan and Tajikistan - that also comprise the SCO - are also taking part in the annual military training exercise.
The two-day military medicine conference in New Delhi is being held in accordance with the SCO Defence Co-operation Plan 2019-20. Apart from the SCO nations save Pakistan, Sri Lanka and Nepal are participating as dialogue partners.
Defence Minister Rajnath Singh inaugurated the conference earlier on Thursday where he stressed upon the need for armed forces to develop capabilities against the threat of bio-terror.
"I would like to underline the importance of building capabilities to deal with the menace of bio-terrorism. Bio-terror is a real threat today. It breaks out as a contagious plague and the armed forces and its medical services have to be at the forefront of combating this menace," he said.