"Pakistan strongly condemns the bomb blasts in Hyderabad, India, last night causing several deaths and injuries," Foreign Office spokesman Moazzam Khan said in a statement.
"Terrorism in all its forms and manifestations constitutes one of the most serious threats to international peace and security. All acts of terrorism are unjustifiable regardless of their motivation," he said.
As a victim of terrorism, Pakistan "fully understands and shares the pain and agony of the people of India".
Two powerful blasts in a crowded area close to a cluster of bus stands in Hyderabad killed 16 people and injured over 100.