There is no problem getting a visa at Manas airport. Prices are US$36 for a 30 day entry and US$55 for over 30 days.

Unexpected 'fees': If you are suddenly asked for an unexpected 'entrance fee' or 'tax' (eg. at border crossings, nature parks, etc.), there's a quick way to see if it's a legal one or merely a bribe: ask for a receipt. Normally, an official receipt (which is 'kvi-TAN-tsia' in Russian) should be printed and stamped by the concerned authority, not merely hand-written on a grotty piece of paper. Of course, if they're reluctant to give you one it's more likely that they're just out for backsheesh.

Permits
# OVIR Registration. It is required to register with the Office of Visa and Registration Department (OVIR), within 3 business days after arrival in Kyrgyzstan.
# Special Permits: There are some regions in Kyrgyzstan that one can't access without a special permit. Those regions, in particular, are: Inylchek glacier, Terskey Alatau, Lenin Peak region, Turkestanskij and Alaiskiy Ranges, Chatkal valley. The permits are issued by the Kyrgyz Agency for Tourism and Sport and can be obtained by your local agency.

To learn more you can also visit such a useful link:
http://www.lonelyplanet.com/destinations/central_asia/kyrgyzstan/
useful info about Kyrgyzstan