"If we are faced with a situation where the energy chapter is blocked, we would of course review our position [on Nabucco]," he said at a conference organised by the Brussels-based European Policy Centre think-tank.
"The other side [the EU] ought to be fair in its treatment," he added.
According to Mr Erdogan, EU member Cyprus "is putting pressure" on the other 26 member states "so that some chapters are not opened, such as energy."
A Czech EU presidency official told EUobserver that there was still "no unanimity" among member states on this "complex chapter," but added that the presidency is working in order to obtain consensus.
The European Commission considers the energy chapter ready for opening and says it is up to member states to give the green light.
Eight other chapters of Turkey's EU accession package have been officially blocked since 2006 as a result of Ankara's refusal to open its ports to Cypriot ships, despite signing a protocol in 2005 to extend its customs union with the EU to the 10 states that joined the bloc in 2004.
Turkey does not recognise the Greek Cypriot government in the southern part of the divided island, while at the same time being the only country to recognise its northern Turkish Cypriot section.
Ankara says that due to this "political issue," Cyprus is also blocking the opening of other negotiating chapters.
Energy - a means to woo EU public
Speaking at a joint press conference with Mr Erdogan later on the same day, European Commission President Jose Manuel Barroso said: "We agreed on the need for this [Nabucco] pipeline and we should solve quickly the outstanding problems."
The Nabucco plan proposes a 3,400-km pipeline from Turkey's eastern border to Austria that would transport up to 31 billion cubic metres of gas per year from Azerbaijan, Turkmenistan and Iran. It is seen by the EU as a key tool to diversify gas supplies in the wake of the current Russia-Ukraine gas crisis.
"We should see our energy relations not only in the framework of the accession negotiations," Mr Barroso added, calling energy supply a "critically important" issue.
The commission president said that energy security was an area where Turkey "could make the case in [EU] public opinion," which remains mostly sceptical towards Ankara's EU future.
"This is one of the cases where we can show to the European Union public opinion how important Turkey is for the EU ...Turkey should not be seen as a burden, but as an asset," Mr Barroso said.
For his part, Mr Erdogan softened his earlier speech saying: "We give full support [to Nabucco] all the time," but once again called for "political obstacles" to be removed and accession talks to be sped up.
'A leap' expected in 2009
Despite the slow pace of negotiations, Mr Erdogan stressed EU integration remained a "top priority" for his country and expressed hopes this year would bring positive developments in the process.
"I hope there will be a leap in 2009," Turkey's premier said.
"There has been a lot of negativity coming out of Europe about Turkish membership and this has affected levels of public support in the country," which fell from 75 percent in 2004 to 40-50 percent at present, he warned.
Turkey opened EU accession negotiations in 2005. It has so far opened ten of its 35-chapter accession package, with just one successfully closed.