Poland also insists that Russia lift the year long ban on Polish food imports which it believes is politically motivated.
Russian President Vladimir Putin refused to sign the charter at an informal EU gathering last month in Finland.
EU High Representative for Common Foreign and Security Policy, Javier Solana told Radio Free Europe/Radio Liberty that he had no doubt an agreement will be reached and that Poland's concerns are already under discussion.
"Russia has said many times that they are not against the philosophy of the charter, but they have some difficulties in accepting the manner in which these ideas are expressed," said Solana.
The charter, among other things, would commit Russia to providing reliable access to energy supplies and pipelines, security of investments and transparency within the massive Russian energy market.
Instead Putin said Russia preferred to deal bi-laterally with the EU member states on energy issues. This has unnerved many countries in the EU , which is largely dependent on Russian energy supplies.
Few EU members agreed with new member Poland on November 13, 2006. Neighbouring state Lithuania was one of few members to offer words of support.
In July, Russia stopped supplying oil to Lithuania's Mazeikiai refinery, the largest in the Baltic states just months after it was bought by the Polish firm PKN Orlen. This is the kind of energy blackmail that Poland, Lithuania and allies fear from Russia.
The Baltic states and Poland have been alarmed by Russia who circumvented them by building the Nord Stream oil pipeline directly under the Baltic sea to Germany.
Many accuse Russia of using energy as a weapon of political pressure.
The Russian envoy to the EU Vladimir Chizhov said that Poland, by issuing such an unpopular ultimatum to its EU partners has proved that EU enlargement was a mistake.