European Union foreign ministers reached a deal with Cyprus, which had been refusing to agree to negotiations unless Turkey recognised the Greek Cypriot government and fully implemented the so-called Ankara protocol, which requires Turkey to open its ports and airports to traffic from the 10 new EU member states, including Cyprus.
An EU official, after discussions with new member Cyprus, said: "We have agreed a common position on Turkey."
Abdullah Gul, the Turkish foreign minister, had refused to travel to Luxembourg until the situation was sorted out.
After the decision, he met his advisers to assess whether the EU's stance was acceptable to Turkey.
The deal means that Turkey will be able to complete the first of 35 detailed policy negotiations on science and research. This is possibly the least contentious of the policy "chapters" to be covered during negotiations, which are expected to last at least 10 years.
Turkey will not have to recognise Greek Cyrpus immediately but will be told that the EU expects it to recognise all member states during the accession process.
"Failure to implement its obligations in full will affect the overall progress in the negotiations," said the EU text to be incorporated into the agreement on science and research.
Ankara was told in October that it would be able to begin membership talks after the EU overcame objections from critics that wanted Turkey to be offered a "privileged partnership" rather than full EU membership.
Turkey argues that recognition of the Greek Cypriot government is linked to a UN-sponsored peace plan to reunite the divided island, which Turkish Cypriots accepted but Greek Cypriots rejected in 2004.
Cyprus has been divided since 1974 when Turkey occupied the north of the country in response to an Athens-engineered Greek Cypriot coup seeking to unite the island with Greece.