The council statement was issued hours before U.S. President Donald Trump meets China's President Xi Jinping at his Florida resort, where North Korea will be at the top of the agenda.
Abe said the two leaders agreed that North Korea's latest ballistic missile launch was a "dangerous provocation and poses a great threat to Japan's national security".
In February the North simultaneously fired four ballistic missiles off its east coast, three of which fell close to Japan.
South Korea has successfully test launched a new, homegrown 800-kilometer-range ballistic missile.
On Thursday (6 April), senior officials and leaders from South Korea, Japan and United States discussed North's missile launch.
European Union sanctions against North Korea date back to 2006 and are part of worldwide efforts to halt a nuclear and ballistic missile programme which experts say is meant to give Pyongyang the capability to hit the United States mainland.
"The government strictly protested and strongly condemned it", Yoshihide Suga, the chief cabinet secretary, said.
Despite angry opposition from Beijing, the USA last month started to deploy the first elements of THAAD in South Korea.
"As adversaries continue to pursue credible and advanced capabilities, we too must evolve our missile defence capabilities to outpace increasingly complex threats", she said.
The projectile could play a key role in the South Korean plan known as Korea Massive Punishment and Retaliation, or KMPR, which could target the North Korean leadership in the event of a nuclear attack.
"The launch took place possibly in consideration of the US -China summit, while at the same time it was to check its missile capability", a South Korean official told Reuters about the military's initial assessment of the launch.
North Korea's foreign ministry on Monday criticised the U.S. for its tough talk and for an ongoing joint military exercise with South Korea and Japan which the North sees as a dress rehearsal for invasion. "Both agreed to push forward the deployment of THAAD by US forces in Korea".
Thursday's statement came as Washington seeks to ramp up pressure on Beijing to exert influence over Pyongyang. Others attribute North Korea's unsuccessful launches to poor-quality missiles, unreliable equipment, and incompetence. North Korea sees the drills as an invasion rehearsal.
In brief comments televised nationally, Abe also said Trump had told him all options were on the table.