The visit comes as U.S. officials are discussing with Afghan officials a possible U.S. military presence in Afghanistan beyond 2014, which would require using Kyrgyzstan's Manas airbase after the current rental agreement expires.
Panetta, speaking to reporters aboard his plane to Bishkek, said he would talk to Kyrgyz leaders about the "importance" of Manas and "ensure that the relationship can continue into the future."
Officials said Panetta was expected to hold talks with Kyrgyz Defense Minister Taalaibek Omuraliev. No meeting with Kyrgyz President Almazbek Atambaev was announced.
Last month, Atambaev told visiting U.S. State Department officials that "no foreign troops" should remain at Manas after 2014.
The U.S. military pays Kyrgyzstan to use facilities at Manas as a transit center for international operations in Afghanistan. The U.S. military reportedly has some 1,500 personnel at the facility.
Officials said Panetta is stopping in Kyrgyzstan on his way to Afghanistan.