The independence decree will force Ukrainian clerics to pick sides between the Moscow-backed Ukrainian churches and the new church as fighting persists in eastern Ukraine between government forces and rebels backed by Russian Federation.
Since the February 2014 coup, Kiev has sought to create an independent church in Ukraine that would sever ties with the canonical Ukrainian Orthodox Church.
Poroshenko, who is up for reelection at the end of March, has made the creation of the independent church a part of his campaign platform.
Nevertheless, after the council, the Ukrainian president announced the establishment of this new church in the country.
Last month, Ukrainian Orthodox leaders approved the creation of a new, unified church split from the Moscow Patriarchate and elected Metropolitan Epiphanius to lead it.
The Orthodox Church of Ukraine was formally granted independence at a ceremony in Istanbul on Saturday, completing a historic split from Russian religious control that had been ongoing since 1868. "(It) will make Moscow's hope of some future pull of Ukraine back into its "orbit" nigh on impossible without the use of overwhelming (catastrophic) military force".
The Patriarchate of Moscow has more followers than the Patriarchate of Constantinople and has challenged it for authority in the past.
Kiev claims Moscow-backed churches in Ukraine are a Kremlin tool to spread propaganda and support fighters in the east in a conflict that has killed more than 10,000 people. The churches strongly deny this.
The ceremony on January 5 in Istanbul, which is considered the spiritual headquarters of Orthodox Christianity, was attended by Ukrainian President Petro Poroshenko. "It was signed in breach of canonicity and this is why it has no power", Vladimir Legoida, the head of the Russian Orthodox Church Synodal Department for Church-Society and Media Relations, posted in Telegram messenger.
The Ecumenical Patriarchate first agreed to recognise the independence of the Ukrainian Orthodox Church in October.
Meanwhile, Putin said: "I think Bartholomew's main incentive and motive is to subdue this territory and then start profiting from it". Infuriated, the Russian church broke ties with the patriarchy in Istanbul, the center of the Orthodox belief for some 300 million Christians worldwide.
Ihor Guskov, the SBU's chief of staff, said the cleric was suspected of "inciting hatred".