South Ossetia and Abkhazia in Georgia and Transdnestr in Moldova declared independence in the early 1990s following the collapse of the Soviet Union. Russian troops assisted ceasefire agreements in these republics and have helped maintain a ceasefire since then.
However, West-leaning central authorities in Moldova and Georgia have recently been seeking expulsion of Russian forces from the conflict zones.
"We will call on the international community to avoid dangerous trends of applying double standards in approaches to these republics' problems," Putin told a Web cast.
When asked whether it was possible to hold independence referenda in the breakaway republics, the president said Russia respected territorial integrity of Georgia and Moldova.
"But it is also important to respect the opinion of people living in these territories," he said.
Putin said there had always been a contradiction in the principles of international law and it remained at present.
"[Russia] wants and will insist on such decisions to be based on a universal principle to prevent such cases when approaches to the regions like Kosovo are different from those to Abkhazia or South Ossetia, which is incorrect," Putin said.