Ministry spokesman Emmanuel Nahshon told journalists that the EU's Federica Mogherini said the European Union's November decision to label goods imported from Jewish settlements "does not prejudge the outcome" of the conflict.
"The conversation resolved the tensions and we are, Israel and the EU, back to good and close relations," Nahshon wrote in an English-language comment on social media.
On November 11, Netanyahu, who is also foreign minister, ordered the freeze in response to an EU directive to member governments to label settlement produce imported to Europe as such rather than "Made in Israel".
Netanyahu flies to Berlin on Tuesday at the head of a ministerial delegation for talks with German Chancellor Angela Merkel and members of her cabinet.
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US-backed peace talks between the Palestinians and Israel collapsed in April 2014 after nine months of fruitless meetings amid bitter recriminations.
A wave of violence which erupted on October 1 has claimed the lives of 26 Israelis, as well as an American, a Sudanese and an Eritrean, according to an AFP count.
After meeting in Munich today with fellow members of the international Middle East peacemaking Quartet, Mogherini said the group planned to draft "a report on the situation on the ground".
"We want it to be not only a report on the state of play, but with recommendations," for progress toward establishing an independent Palestinian state alongside Israel, she told journalists.
She would also speak later today with Palestinian president Mahmud Abbas, "to make clear that the international community will not give up on the two-state solution".