He added there is "absolute reassurance between the two of us that we stand firm" and the relationship will not be affected by the denuclearisation talks.
Speaking at an international security conference in Singapore, Mr Onodera said North Korea agreed to give up nuclear weapons as early as 1994, but has continued to develop them in secret and until last year threatened surrounding countries with a series of ballistic missile launches.
On Friday, he said the US and Japan must work together towards the dismantlement of "all of North Korea's weapons of mass destruction, including biological and chemical weapons and ballistic missiles of all ranges".
Mr Mattis said the two discussed "the opportunities to increase our alliance capabilities, to deepen our co-operation and to enhance regional security".
On Thursday, Mr Mattis met with South Korean defence minister Song Young-moo, assuring him the US will maintain its current number of troops on the Korean Peninsula (Picture: US Department of Defense).
Speaking alongside Mr Song, Mr Mattis read a lengthy statement reinforcing America's "ironclad" commitment to Seoul, adding that "the US will continue to use the full range of diplomatic and military capabilities to uphold this commitment".
After their meeting, Mr Onodera said they agreed to continue joint military exercises and reinforce the response capability of the US-Japan alliance.
The US and Japan, he said, agreed to work with other countries to tackle offshore ship-to-ship transfers by North Korea that may evade economic sanctions.
Japan's navy has been actively watching for and submitting photographic evidence of possible sanctions violations to the UN.