The EU has opened a new stage of membership talks with Turkey, three months after imposing a partial freeze.
Mr Babacan said Turkey would carry out reforms independently
The two sides started talks in a second of 35 policy areas, which Turkey has to complete - showing that it meets EU standards - before it can join the EU.
Last December the EU froze talks in eight areas, calling on Turkey to open its ports to Cypriot ships.
Turkey said on Thursday that it would announce plans next month to carry out all the necessary reforms anyway.
"We will be announcing a programme by which we will be continuing our reforms and this programme will cover all the 35 chapters, even those chapters which will not be opened because of issues... relating to Cyprus," said Turkey's EU negotiator, Ali Babacan.
The EU's December decision to slow down membership talks also stipulated that no chapters of the talks would be completed until Turkey allowed Cypriot ships into its ports, and Cypriot aircraft into its airports.
But Mr Babacan said there would be no progress on this issue until the European Union honoured a 2004 decision to end the economic isolation of the Turkish Cypriot community.
The European Commission drafted a regulation in 2004 that would kick-start direct trade between the Turkish Cypriots and the EU, but the Cypriot government has reportedly blocked its adoption.
Foreign ministers agreed in January that "work aiming at the adoption of special conditions for trade" with the Turkish Cypriots "must resume without delay".
However, an EU official quoted by the AFP news agency said the Republic of Cyprus was "totally intransigent on direct trade" and that no progress was likely until after presidential elections there in 2008.
German Foreign Minister Frank-Walter Steinmeier welcomed the opening of the new chapter of Turkey's accession talks.
He added that the German EU presidency was aiming to open several chapters before the end of June.
Mr Babacan said the EU's decision to partially suspend Turkey's membership talks had triggered some disillusionment in Turkey, and that it was crucial to show Turkish citizens that the accession process was moving forward.
He said the reform programme that Turkey was about to announce would bring the country into alignment with EU requirements in all 35 policy areas, by 2013.
Cyprus has been divided since 1974, when Turkey seized the northern third of the island.
It was acting in response to a Greek-inspired coup in Nicosia, aimed at uniting the island with Greece.