The talks, scheduled to start on 24 June, can take place after council finally agreed its mandate for negotiation following the adoption of parliament's position by the civil liberties, justice and home affairs (LIBE) committee in March 2014.
Parliament has repeatedly urged council to move ahead as the EU's current legislation dates back to 1995, leaving European citizens' data protected by rules drafted before the arrival of the digital age.
German Greens MEP Jan Albrecht, who is parliament's rapporteur on the data protection regulation, welcomed the move, saying, "After over a year of stalling, it is encouraging that we can finally push ahead with the EU data protection reform and that parliament can begin negotiations with the council."
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"The challenge is now to reconcile the two sides, to ensure that the reform provides reliable and high common standards of data protection, and reach an agreement on this before the end of the year.
"There are clearly differences, notably on consumer rights and the duties of businesses. However, if we can negotiate constructively and pragmatically, it should be possible to deliver a compromise acceptable to both sides within the timeframe. This outcome would benefit everyone and show that the EU takes the concerns of its citizens in the digital age seriously."
The three-way talks will be overseen by chair of parliament's LIBE committee Claude Moraes, a UK Socialist, who said, "Despite the difficult negotiations involved, the parliament, led by the rapporteur Jan Albrecht, will work towards finding a swift agreement on the data protection regulation by the end of 2015 which will set out a robust, modern, consistent and higher level of protection for the years to come."
The data protection regulation is part of a package which includes a directive and Moraes urged European ministers to also "ensure that they find agreement on the data protection directive for law enforcement by October 2015 as the parliament's position has always been clear that we treat both proposals as a package".