Petro Poroshenko’s elected pro-Russian predecessor, Viktor Yanukovych, was overthrown in February after refusing to sign the deal at the last moment.
Heavy fighting has erupted between troops and pro-Russian rebels in Donetsk region despite talk of a truce.
Meanwhile, NATO says Russia has moved troops back to the Ukrainian border.
Petro Poroshenko was elected president in May on a pro-EU platform after six months of political turmoil.
Since Viktor Yanukovych fled Kiev, Russia has annexed part of Ukraine’s territory, Crimea, and has also been accused of stoking the rebellion in the east.
According to a UN estimate reported this week, at least 356 people, including 257 civilians, have been killed in eastern Ukraine since May 7.
Political parts of the association agreement were signed in March by Ukraine’s interim government.
Petro Poroshenko made the announcement as he was replacing three senior officials in Kiev.
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