"We have agreed to meet as part of the commission, which we once created but, unfortunately, have not yet been able to launch," Putin told Oleksandr Moroz, the speaker of the Ukrainian parliament.
Putin said a number of economic agreements should be reached and regular political contacts maintained to ensure the effective work of the commission.
Major stumbling blocks in bilateral relations include the Russian Black Sea Fleet based at the Crimean port of Sevastopol, and the demarcation of the Sea of Azov and the Kerch Strait.
The price of Russian natural gas, an important factor for Ukraine's economy, has also been a contentious issue between the ex-Soviet neighbors.
After Russian energy giant Gazprom sought a significant increase in the price it charged Ukraine for Russian gas at the end of last year, Kiev retaliated by threatening to increase the rent it charges for the Russian Black Sea Fleet to $1.8 billion.
Russia, however, insists that an agreement signed by the two countries in 1997, which divided the Soviet Black Sea Fleet, stipulates that the Russian Navy is to remain in Sevastopol until 2017 at an annual rent of $93 million.
The confrontation over the Russian-Ukrainian border through the Azov and Black Seas and the Kerch Strait erupted in summer 2003 when Russia attempted to construct a dam on the Tuzla Island in the Kerch Strait. Ukraine accused Russia of encroaching onto its territory, and deployed border guards on the small island.
Moscow has been hopeful for a resolution of bilateral disputes with Kiev since Viktor Yanukovych, the leader of the pro-Russian Party of Regions, became Ukrainian prime minister in August.
