The agreement provides that a land plot of five hectares (12 acres) at the Kant Russian military base in Kyrgyzstan will be used for the joint programme.
"Lawmakers examined and adopted the bill on the ratification of the agreement between the Kyrgyz Republic and the Russian Federation for the creation of a Joint Regional Air Defense System," the Kyrgyz parliament said.
Putin had been scheduled to travel to Kant, but the Kyrgyz presidency told AFP Wednesday the visit had been cancelled, without providing more details.
The Russian leader is still due to speak with his Kyrgyz counterpart Sadyr Japarov on Thursday, and attend a summit gathering leaders of post-Soviet countries the following day.
The agreement for a shared defence system between their two countries is valid for five years, Russian state-run news agency RIA Novosti reported.
Russia has similar deals with other allied countries including Kazakhstan, Belarus or Tajikistan.
The announcement comes as Moscow's Collective Security Treaty Organization (CSTO) comprising six post-Soviet states has been criticised over the past few months.
CSTO members pledged to protect each other in case of an attack but Moscow refused to intervene when Azerbaijan launched an offensive on the ethnic Armenian separatist statelet of Nagorno-Karabakh.
The alliance has not sent peacekeeping troops to prevent border clashes between Kyrgyzstan and Tajikistan, both members.
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