The Nimitz-class aircraft carrier is undergoing scheduled maintenance at its home port.
Pence told the ship's captain that he had spoken to President Donald Trump, and Trump "wishes he were here".
Like South Korea, Japan already faces a direct threat from the secretive regime.
Despite the tension, North Korea may carry out a sixth nuclear test soon, observers say. The tests have grown in sophistication each time, U.S officials said.
"It is our belief by bringing together the family of nations with diplomatic and economic pressure we have a chance of achieving a freeze on the Korean Peninsula", Pence said.
On April 15, the U.S. Navy published a photo showing the aircraft carrier USS Carl Vinson transiting the Sunda Strait between the Indonesian islands of Java and Sumatra. Last week, Trump said he would not declare China a currency manipulator, pulling back from a campaign promise, as he looked for help from Beijing, which is the North's dominant trade partner.
He also said it was reassuring that Mr Pence had not cited trade reforms as a pre-condition for the US-South Korea military alliance.
It's Tokyo's oldest temple, and a highly popular tourist site that attracts crowds from around the world.
Pence's trip will also include stops in Indonesia, Australia and a visit with US troops in Hawaii.
Last week, President Trump said that he hadn't realized how hard it would be to disarm North Korea until he received a short history lesson from Chinese President Xi Jinping.
"North Korea is going to overshadow his first two stops; he will be wanting to explain to both our allies the perimeters of the recently completed trump policy on North Korea".More news: Markets Right Now: Health care, banks lead US stocks lower
The vice president spoke at a news conference following the Japan-U.S. economic forum in the afternoon with Deputy Prime Minister Taro Aso.
"All options are on the table", Pence said.
Japan and the US have outlined a path forward for economic talks between the countries.
"The talks Tuesday did not delve into sector-by-sector issues such as auto exports".
The vice president met Japanese officials, including Prime Minister Shinzo Abe, and reassured them of the United States commitment in the face of possible threats posed by North Korea.
US President Donald Trump took a moment at the White House Easter egg roll Monday to deliver a terse message to North Korean leader Kim Jong-Un: "Got to behave".
"The United States will strengthen its presence in the Asia Pacific", he said.
Abe said Japan likewise hopes for peaceful dialogue with Pyongyang, "but at the same time, dialogue for the sake of dialogue is valueless".
"President Trump has made it clear that the patience of the United States and our allies in this region has run out and we want to see change".
At a working lunch with Japanese Prime Minister Shinzo Abe, the two leaders said they will urge China to do more to rein in Pyongyang, which launched a missile unsuccessfully on Sunday, a day after unveiling what appears to be new missiles.