President Donald Trump on Tuesday said "all options are on the table" in response to North Korea after the isolated nation escalated tensions by firing a ballistic missile that passed over Japan.

"The world has received North Korea's latest message loud and clear: this regime has signaled its contempt for its neighbors, for all members of the United Nations, and for minimum standards of acceptable international behavior," Trump said in a statement.

"Threatening and destabilizing actions only increase the North Korean regime's isolation in the region and among all nations of the world. All options are on the table," he added.

The latest test puts the United States and its allies in a difficult spot as they aim to curb Pyongyang's nuclear and missile programs. They have aimed to pressure North Korea through international sanctions and other economic pressure from China, North Korea's only major ally.

Though the U.S. has said it prefers a diplomatic solution, Trump has previously left the door open for "all options." Earlier this month, Trump promised "fire and fury like the world has never seen" if North Korea continued to threaten the U.S. and its allies.

Trump spoke to Japanese Prime Minister Shinzo Abe on Monday night after the missile flew over Japan. They agreed that Pyongyang "poses a grave and growing threat" and "committed to increasing pressure on North Korea," according to a White House readout of the call.

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

Nikki Haley, U.S. ambassador to the United Nations, on Tuesday said the U.S., Japan and South Korea have called for an emergency meeting of the organization's Security Council.

Haley said "something serious has to happen," adding, "enough is enough."

On Monday night, Japanese broadcaster NHK reported that the Japanese government warned that a North Korean missile was headed toward the Tohoku region at the northern end of the country. NHK also reported that Japan took no action to shoot down the missile.

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

While the U.S. Department of Defense said it is still assessing the missile launch, the North American Aerospace Defense Command determined that it did not pose a threat to North America.

A senior U.S. intelligence official told NBC that this would be the first missile test to pass over Japan on a high-altitude trajectory. In 1998, North Korea fired a missile through Japanese airspace.

Trump first made his "fire and fury" threat after reports that Pyongyang had successfully miniaturized a nuclear weapon that could fit in one of its missiles. He later suggested that the statement did not go far enough.

U.S. stock futures fell sharply after North Korea launched its missile. Dow Jones industrial average futures pulled back more than 100 points, while S&P 500 futures declined 13 points.

— CNBC's Christine Wang and Fred Imbert contributed to this report.