Declaration that would allow talks on Turkish accession to EU was rejected by Ministers from EU member states.
The text agreed by diplomats on Monday was pulled from the agenda of ministers meeting in Brussels at Cyprus' request.
It says Turkey must formally recognise Cyprus before joining the EU. Diplomats said Cyprus did not object to the text itself but was delaying approval until agreement on a negotiating mandate for the talks, according to Reuters.
Both the declaration and the negotiating mandate must be settled before the talks can begin on 3 October.
It is a response to a statement by Turkey in July, refusing to recognise Cyprus, despite the extension of its customs union with the EU to all new member states.
This date was agreed by the EU last December, and any delay would be a serious embarrassment.
On Monday, EU ambassadors agreed a draft declaration which said: "Recognition of all member states is a necessary component of the accession process."
It also stressed the importance of the "normalisation of relations between Turkey and all EU member states, as soon as possible". Nicosia had reportedly been lobbying for Turkey to be given a specific deadline to recognise Cyprus, but on Monday apparently withdrew this demand, BBC says.
However, Cypriot President Tassos Papadopoulos muddied the waters on Tuesday saying that the EU declaration called for a review of the question of Turkish recognition of Cyprus in 2006.
He also said the UK was attempting to link recognition with an agreement to end the island's division, as Turkey has demanded. Discussions on the negotiating framework are expected to focus on Austria's view that it should leave open the possibility of offering Turkey a "privileged partnership" instead of full membership.
Earlier agreements have made it clear that the goal of the talks would be full membership.