Atambayev will be accompanied by a high-level delegation comprising senior ministers, top officials and business leaders.
It will be first presidential visit from the key central Asian nation to India in 13 years and Atambayev's first trip here as President.
Joint Secretary (Eurasia) in the Ministry of External Affairs G V Srinivas said bolstering existing defence cooperation, enhancing trade ties and exploring surface connectivity projects will be high on the agenda of talks between the Prime Minister and the Kyrgyz leader.
Besides joint military exercises, the two countries have been cooperating on high-mountain biomedical research to know impact on soldiers when they carry out operations at high altitude.
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Relations between India and Kyrgyzstan have been on an upswing and the country has supported India's bid for membership of the UN Security Council as well as its entry into the Shanghai Cooperation Organisation (SCO).
Talking about Kyrgyzstan's strategic location, Srinivas said its distance from India is just 1,600 km and both the countries were keen to have surface connectivity to boost trade relations.
During the visit, Atambayev is expected to attend a Joint Business Forum being organised by industry chambers FICCI, CII and Assocham.
"India and Kyrgyz Republic share excellent relations marked by strong ties in all areas including political and defence, economy and commerce, education and human resource development, culture and tourism," MEA Spokesperson Vikas Swarup said.
He said the visit will further cement the traditionally cordial and close ties between the two countries.
A sizeable number of Indian students study in that country. Telemedicine and medical tourism are two areas which have seen significant growth in the past few years.