The complaint came after Kazakh President Nursultan Nazarbayev met with opposition candidate Omurbek Babanov, competing in the country's strongly contested October election.
In an angry note to Kazakhstan's ambassador, the Kyrgyz foreign ministry expressed "bewilderment" at the meeting, which it characterised as "an expression of support".
It said it regarded the meeting as an "attempt to influence the choice of the people of Kyrgyzstan and interference in the internal affairs of the Kyrgyz Republic".
Kazakhstan said today it was "extremely surprised at the reaction", adding that Nazarbayev regularly meets politicians from other countries.
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Kazakhstan's Nazarbayev, 77, is the only incumbent president in the former Soviet bloc that assumed control over his country before the bloc's collapse and oil profits have helped entrench his authoritarian rule.
Resource-poor Kyrgyzstan is seen as the most democratic state in Central Asia, a predominantly authoritarian region, but it has also been the most politically volatile in recent times.
The Muslim-majority country experienced two revolutions that unseated presidents in 2005 and 2010 followed by ethnic violence that left over 400 people dead.
Two opposition politicians that would otherwise have been on the 13-candidate ballot were sent to prison on corruption and kidnapping charges earlier this summer.
Former oil trader Babanov, widely viewed as the wealthiest candidate, will face competition from outgoing president Almazbek Atambayev's prefered choice, friend and ally Sooronbai Jeenbekov.
Jeenbekov and Babanov both served as prime ministers over the course of Atambayev's six-year term which he is constitutionally prohibited from extending.