The launch took place at 5:30 a.m. local time, according to a statement from the South Korean Foreign Ministry.
North Korea's launch took place in the waters, off Sinpo, South Hamgyong Province, in the early morning, the South Korea's Joint Chiefs of Staff said.
"If the North Korean regime continues to pursue its nuclear and missile capabilities and ignore severe economic difficulties of its people, it will bring about more severe sanctions and diplomatic isolation. It should also realize that it will hasten its self-destruction," the country's Foreign Ministry said.
"Our government is prepared with full readiness posture to protect our people and the safety of our country and will thoroughly respond to any North Korea's provocation."
The US Pacific Command tracked the missile over and into the Sea of Japan, also known as the East Sea, approximately 300 miles off the coast of North Korea.
This was the first time a North Korean missile entered Japan's air defense identification zone, Japanese Prime Minister Shinzo Abe said.
"This is a threat to Japan's security and an unforgivable reckless act that significantly damages the peace and stability of the region," Abe said Wednesday morning.
The launch comes amid the annual joint military exercise between the United States and South Korea, which kicked off on Monday.
The annual drill includes 25,000 US troops, the bulk of which are already stationed in Korea, according to a statement by US Forces Korea.
Compared to previous tests, Wednesday's missile is seen as "an improvement," according to the South Korean Joint Chiefs of Staff. The United States and South Korea are closely analyzing the details.
Dr. Daniel A. Pinkston, a professor at Troy University, told CNN the fact that the rocket traveled as far as it did suggests the North Koreans are "making quite rapid progress, and probably more rapid progress than any people had predicted."
North Korea's latest military move has drawn condemnation from the South Koreans.
This as a "serious challenge against the security of the Korean peninsula" and believed to be "part of North Korea's armed protest to escalate military tension in the Korean peninsula using annual US-South Korea joint drill as an excuse," the South Korean Joint Chiefs of Staff said in a press statement.
A senior US State Department official told CNN the US is trying to determine whether the launch was successful.
The missile is presumed to be a KN-11, said Navy Cmdr. Dave Benham, a spokesman for US Pacific Command.
Threat of more missiles
North Korea has made threats of nuclear retaliation if the two-week drills "show the slightest sign of aggression
," a spokesman for North Korea's military was quoted as saying by the country's state media.
In response to the joint drills, North Korea on Tuesday sent a letter to the UN Security Council, complaining that the "US-led large-scale joint military exercise in collusion with the south Korean forces despite repeated warnings of the DPRK is a grave military provocation aimed to launch a preemptive nuclear attack on the DPRK and a challenge to regional peace and stability in every way."
Under Security Council resolutions, aimed partially at curbing North Korea's development of nuclear weapons, the communist country is prohibited from carrying out ballistic missile launches.
A South Korean defense official earlier this month said North Korea has launched more than 30 test missiles since Kim Jong Un, the country's leader took power in 2011.
Though North Korea has aimed to improve its nuclear and missile capabilities, it has yet to pair the two successfully.
The US Strategic Command said one of the missiles exploded after launch. The other flew about 621 miles (1,000 kilometers) over North Korea and into the Sea of Japan, according to the South Korean Joint Chiefs of Staff.