The firing comes days after Pyongyang launched three short-range missiles in what was seen as a minimal provocation after the start of the Ulchi Freedom Guardian South Korean-US joint military exercises.
But Tuesday’s flight path represents a significant escalation by Pyongyang, which earlier this month threatened to fire a salvo of missiles towards the US territory of Guam.
Any such flights would have to pass over Japan.
“North Korea launched a ballistic missile which appears to have flown over Japan,” Abe said in televised comments.
“We will immediately collect and analyse details and the government will take full steps to protect Japanese people’s lives.”
The “unidentified ballistic missile” was launched at around 2057 GMT Monday from Sunan, near Pyongyang, the South’s Joint Chiefs of Staff said in a statement, saying it travelled east “and over Japan”.
Japan’s top government spokesman said the missile flew over the country’s northernmost island Hokkaido and then fell into the Pacific, some 1,180 kilometres (733 miles) east of the coast.
“So far no fallen objects have been confirmed to have fallen inside Japanese territory,” Chief Cabinet Secretary Yoshihide Suga told an emergency press briefing.
“There is no report of damage to aircrafts and vessels” in the area, he added.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)