Mr Abe on Saturday called the failed test "absolutely unacceptable" and a "grave threat to our country", as he spoke at the end of his three-day visit to Russia and Britain, the Daily Mail reported.
One of Tokyo's major subways systems shut down all lines for 10 minutes after receiving warning of a North Korean missile launch.
Tokyo Metro official Hiroshi Takizawa said the temporary suspension affected 13,000 passengers on Saturday morning.
Mr Takizawa said it was the first time service had been stopped in response to a missile launch.
Train services are generally suspended in Japan immediately after large earthquakes.
Earlier on Saturday, North Korea launched a ballistic missile that blew up over land.
The main part of the missile landed approximately 35 km from Pukchang airfield, north of Pyongyang, according to CNN.
South Korea's Joint Chiefs of Staff said the missile flew for several minutes and reached a maximum height of 44 miles.