The talks focused on the situation in the south of Kyrgyzstan which has recently witnessed violence and unrest between the Kyrgyzs and members of the Uzbek ethnic minority.
The two officials also discussed the role of the media in creating a positive atmosphere ahead of forthcoming parliamentary elections in the country.
Mesic also met with Deputy Foreign Minister Dinara Kamerova and First Deputy Prime Minister Amangeldi Muraliev.
According to the press release, Mesic insisted on individualising guilt and avoiding collective accusations against entire nations.
He also advocated a speedy reconstruction of homes destroyed in the recent riots.
During his stay in Bishkek, Mesic held talks with the US Ambassador to Kyrgyzstan, Tatiana Gfoeller, at her request.