Saudi Foreign Minister Prince Faisal bin Farhan and his Japanese counterpart Yoshimasa Hayashi met in Riyadh on Thursday for their first high-level meeting, official news agency SPA reported.
Among subjects they discussed was Tokyo's decision to offer multiple-entry visas for Saudi citizens who meet certain financial requirement.
Mr Hayashi said Japan attaches great importance to strategic partnerships with Saudi Arabia, reported the agency.
The ministers also discussed joint projects to achieve the vision of making the Middle East the global centre for clean energy supplies and vital minerals.
Japan's environmental credentials have been questioned recently, following the release of treated water from the Fukushima Daiichi nuclear power station, which was destroyed by a tsunami in 2011.
Mr Hayashi defended the discharge, saying it was consistent with the safety standards of intergovernmental nuclear watchdog the International Atomic Energy Agency.
The foreign ministers agreed to continue working on maintaining peace and stability in the Indian Ocean and the Pacific.
Mr Hayashi also met with GCC ministers to discuss co-operation.
The Japanese embassy said Mr Hayashi co-chaired the Japan-GCC Joint Ministerial Meeting with Omani Foreign Minister Sayyid Badr Al Busaidi.
Four foreign ministers – including Prince Faisal – attended, Japanese officials said.