The two leaders met in Russia's Sochi on Tuesday.
"The current Russian [military] presence in Tajikistan is in compliance with international law and bilateral agreements. It is intended to ensure stability and security in this truly tense region," Peskov told reporters.
"There were no agreements yesterday to increase presence there, but Putin and Rahmon agreed that what is happening in Tajikistan and the surrounding areas is a cause of concern," he added.
Both Russia and Tajikistan are participants of the Collective Security Treaty Organization (CSTO), a six-nation military alliance, including Kazakhstan, Kyrgyzstan, Armenia and Belarus. Afghanistan is a CSTO observer state.
Russian Prime Minister Dmitry Medvedev said last month that Moscow is ready to set up military bases to uphold security in other CSTO member nations. Russia currently has airbases in Kyrgyzstan and Armenia.
