Al Khalifa, who is here for the first meeting of the Joint Commission co-chaired by External Affairs Minister Sushma Swaraj, also expressed desire to step up trade and investment between the two countries.
During the meeting with Modi, the visiting minister recalled the "deep emotional bonds of friendship that are felt by the people of Bahrain towards India", a PMO statement said.
"He conveyed the commitment of the government of Bahrain to deepen bilateral relations, including in the areas of defence, security, counter-terrorism, trade and investment," it added.
During the first meeting of the Joint Commission, the issue of terror was on the top of the agenda, External Affairs Ministry spokesperson said.
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Al Khalifa also extended a letter of invitation from his country's Prime Minister to Modi to visit Bahrain.
Modi recalled the visit of the King of Bahrain to India in February 2014 that had provided new vigour and momentum to the bilateral relationship.
He appreciated the continuous support and cooperation being extended by the government of Bahrain to over four lakh members of the Indian community in Bahrain.