Jekshenkulov and his Uzbek counterpart, Vladimir Norov, also signed an agreement on cooperation between their respective ministries and an additional protocol border-checkpoint regulations.
Jekshenkulov is also expected to meet with Uzbek Prime Minister Shavkat Mirziyoev.
Uzbek President Islam Karimov extended the invitation to Bakiev earlier this month.
Uzbek state-controlled media today said the visit will take place in late September.
The two countries have boosted their security ties in recent weeks, vowing to join forces against what they describe as "terror and religious extremism."
Arms and leaflets allegedly confiscated from Hizb ut-Tahrir members in Kyrgyzstan in May (RFE/RL)
ATTRACTIVE TO THE YOUNG: It is virtually impossible to estimate the size or composition of Hizb ut-Tahrir's membership in Central Asia, because the controversial movement is banned in most places. But some observers say anecdotal evidence suggests the group's core of younger members is growing....(more)