It was the first time Tokyo Metro took such a step, following the adoption of new rules this month to stop trains and check for safety in response to news of any missile launches that can potentially hit Japan, local media said.
Trains were stopped at 6:07 am (2107 GMT) after the launch which happened around 2030 GMT, according to national broadcaster NHK.
Around 13,000 people were affected by the halt in service, Kyodo News said.
"It (subway suspension) was a decision of the operator," Chief Cabinet Secretary Yoshihide Suga told a briefing.
"We ask that people stay calm and stay informed. At this time, the latest incident has absolutely no impact on Japan," he said.
The missile launch, which apparently failed, came as Japanese people began the annual Golden Week holiday season.
Japanese Prime Minister Shinzo Abe called Pyongyang's move "absolutely unacceptable" and a "grave threat to our country", speaking in London at the end of a three-day visit to Russia and Britain.
The launch came just hours after US Secretary of State Rex Tillerson warned the UN Security Council of "catastrophic consequences" if the international community -- most notably China -- failed to pressure the North into abandoning its weapons programme.
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