Atambayev, who celebrated his 60th birthday on Saturday, has headed the impoverished Central Asian nation since winning a presidential election in 2011.
In a statement the president's press service said Atambayev began complaining of "chest pains" as his plane made a planned stopover in Istanbul on the way to New York and was urgently examined by doctors.
"According to the preliminary conclusions by the doctors the head of state was found to have symptoms of heart problems," it said, adding that Atambayev would remain under medical supervision for "some time".
Atambayev, who is bound to a single six-year term by Kyrgyzstan's constitution, cuts a different figure from the authoritarian leaders in neighbouring countries.
This year he released a number of acoustic pop songs that his office claimed he composed himself in Kyrgyz and Russian.
His economically troubled country of six million people has seen two governments overthrown and ethnic violence claim hundreds of lives since it gained independence in 1991.
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