A Hwasong-12 medium-range ballistic missile "zoomed to the sky with dazzling flash and big explosion" and "crossed the sky above Hokkaido of Japan along the preset flight track and accurately hit the preset target waters in the Pacific", Xinhua news agency cited the report as saying.
In a statement, Foreign Affairs Secretary Alan Peter Cayetano urged North Korea to "cease its provocative and highly risky actions that threaten the peace, stability and security of the region".
"The Secretary-General calls on the DPRK leadership to cease further testing, comply with the relevant Security Council resolutions, and allow space to explore the resumption of honest dialogue on denuclearisation", Guterres said in a statement, adding that he would discuss it "with all concerned parties in the margins of the upcoming" U.N. General Assembly.
"Of course, we are also concerned about the safety of the 242,000 Filipinos in Japan who may be impacted by these provocative acts", Cayetano said.
Tensions on the Korean Peninsula escalated recently after US President Donald Trump threatened to deal with the DPRK with "fire and fury" last month.
France denounced "in the strongest possible terms", the latest missile launch by North korea over Japanese territory, the country's Foreign Ministry officials said.
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Emmanuel Macron also had a conversation with Emir, the President left the Elysée Palace without speaking to the press. Germany has been supporting diplomatic efforts to try and defuse the crisis.
Seoul's aid to Pyongyang was suspended after the latter conducted its fourth nuclear test in January past year.
The North has confirmed the missile as an intermediate range Hwasong-12, the same model launched over Japan on August 29. Kim said the "combat efficiency and reliability of Hwasong-12 were thoroughly verified, operation members' capacity for actual war is also very ideal and the work for increasing combat power of Hwasong-12 has been realized", according to KCNA.
"The Security Council also emphasized the vital importance of the DPRK immediately showing a honest commitment to denuclearization through concrete action, and stressed the importance of working to reduce tension on the Korean Peninsula", said Tekeda Alemu, president of the Security Council, in a readout of the press statement.
The UN Security Council has accused North Korea of undermining regional peace and security by launching its latest missile over Japan and said its nuclear and missile tests "have caused grave security concerns around the world" and threaten all 193 UN member states.
North Korean leader Kim Jong Un has vowed to achieve the final goal of equilibrium of force with the United States, to make Washington dare not talk about military action against the country.