"This must be stressed ahead of expected worldwide pressure to resume negotiations in light of the Palestinian agreement".
The document was signed on behalf of Hamas by deputy leader Salah al-Aruri, who is responsible for overseeing military operations for the militant group in the West Bank.
Negotiations are now expected to be held on forming a unity government, with the various Palestinian political movements invited to another meeting in Cairo on November 21.
The deal includes 3,000 members of the West Bank-based Palestinian Authority's police force redeploying to Gaza, a member of the negotiating team told AFP on condition of anonymity. The reports also said the Palestinian Authority would seek to merge Hamas' police officers in Gaza with the Palestinian security services.
A reconciliation deal signed by Hamas and Fatah this week not only aims to relieve a decade-long rift between the two Palestinian groups but has also revived hopes of a positive change in the lives of people living in the Gaza Strip. Mogherini made her comment after the main Palestinian factions - Fatah and Hamas - announced an agreement ending the 11-year-old political division.More news: Harvey Weinstein timeline: How the scandal unfolded
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The 2011 agreement stipulated that legislative, presidential and national council elections should be conducted within one year of its signing.
Palestinian media reported that the two sides agreed to form a committee to solve, within four months, one very local problem that has dogged previous attempts at reconciliation: what to do about Hamas bureaucrats who will be out of a job when the Palestinian Authority resumes its rule in Gaza.
He added in a statement, "From now on, any cooperation between Israel and Abbas is cooperation with Hamas".
Islamist movement Hamas is blacklisted as a terrorist organization by the United States and the European Union.
Hamas has said they are not up for discussion, but has assured the Fatah negotiators that the military wing would maintain a low profile as part of any deal.
It has fought three wars with Israel since 2008 and the blockaded Gaza Strip has seen deteriorating humanitarian conditions.