"The contract was signed several years ago. It has not been realised yet," Putin said at a joint press conference with EU leaders. "We do not want to upset the balance in the region."
The Russian leader also warned that any foreign military intervention in the 26-month crisis would fail.
"We once again underscored that any attempts to influence the situation through force and direct military intervention are doomed to failure," Putin said.
Assad's suggestion in an interview last week that one of Russia's most advanced surface-to-air missiles had been delivered to the Damascus regime provoked condemnation from Western nations and fresh expressions of concern from Israel.
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The S-300s could not only theoretically take out Israeli jets that have already made bombing raids over Syria but also complicate any military support missions that Western or regional powers intended to run in the region.
Putin agreed that the S-300 was "one of the best -- if not the best -- air defence systems in the world."
The Syrian crisis and the European Union's decision to lift its arms embargo on Assad's foes dominated the Russia-EU summit that had otherwise been devoted to trade issues.
European Council President Herman Van Rompuy said that Brussels expressed its full support for a joint Russia-US initiative for a peace conference involving both Assad's camp and the opposition to be held as soon as possible.
"What is happening in Syria today is a stain on humankind's conscience," added European Commission head Jose Manuel Barroso.