Bolton first met with Shotaro Yachi, chair of Japan's National Security Council, and later Foreign Minister Taro Kono, Japan's Ministry of Foreign Affairs said in a statement.
"We had a very productive discussion on a wide range of issues," Bolton told reporters following his meeting with Yachi, Kyodo News reported.
During the meeting with Kono, Bolton said that he wants to maintain close cooperation with Japan to resolve issues in the region and reiterated his commitment towards working on North Korean denuclearization, said the statement cited by Efe news.
Issues believed to have been discussed in the meetings include Washington's international coalition plan to strengthen security around the Strait of Hormuz.
The maritime security initiative was drawn up following the attacks on two oil tankers in the region - one of which was operated by a Japanese firm. The US has alleged Iran's role in the attack.
It is estimated that a fifth of the world's oil passes through the Strait of Hormuz.
The White House reiterated that free navigation through the strait was important for global economic stability.
Bolton is to travel to Seoul on Tuesday for a two-day visit and is will meet with his South Korean counterpart Chung Eui-yong, Foreign Minister Kang Kyung-wha and Defence Minister Jeong Kyeong-doo to discuss - among other issues - the current status of denuclearization talks with North Korea.
( With inputs from IANS )