Abe said the missile was an unprecedented, serious and grave threat to Japan. The Japanese prime minister also said he would ask the United Nations to up the pressure on Pyongyang.

North Korea fired a ballistic missile that passed over Japan early Tuesday, and Prime Minister Shinzo Abe had strong words about its gravity.

A South Korean military official told NBC News that the missile was fired around 5:57 a.m. local time on Tuesday. The official said that the missile flew for about 2,700 kilometers (1,678 miles), reaching a maximum altitude of 550 kilometers (342 miles). U.S. Pacific Command projected that the missile splashed down at 6:29 a.m. local time.

Japanese broadcaster NHK reported that the North Korean missile broke into three pieces and fell into the sea.

Here's Abe's full comment when asked what actions his government planned to take, according to NBC News:

The ballistic missile launched by North Korea flew over our nation and landed in the Pacific Ocean. We, as the government, were completely aware of the movement of the missile since immediately after its launch and in order to protect the public we had a well prepared system in place. This reckless act of firing a missile over our nation is an unprecedented, serious and significant threat, one that seriously diminishes the peace and safety of the region, and as a result we have lodged a firm protest against North Korea. We have also requested an emergency meeting of the UN Security Council. By working together with the international community, we will seek to further strengthen pressure against North Korea. Under the firm Japan-U.S. Alliance, so that we can deal with any circumstance, while maintaining a sense of tension, we will do our utmost to ensure the public's safety.

—CNBC's Christine Wang contributed to this report.