The aim of the merger is to win business by having one port tariff to cover several calls at separate terminals.
The move, for instance, will cut the cost of calls for container ships visiting Osaka and Kobe on the same liner service.
Along with a revision of port dues and customs tariff systems, the merger also calls for a service to move containers between terminals.
The new 'super-port' will have a total container throughput of at least 4.3 million TEUs per year, making it Japan's busiest and largest container port, ahead of Tokyo, Yokohama and Nagoya.
Japan's public ports are being restructured to compete with local rivals. Japanese ports have long been criticized for inflexible working hours and high costs.
A senior Japanese official has said Japanese ports risk becoming feeder points for transshipment hubs outside the country.
Ken Abe, a deputy director at Japan's ministry of land, infrastructure and transport, said a growing volume of Japanese cargo was being routed through regional hubs, such as Busan in South Korea.
Abe blamed Japan’s expensive distribution costs and handling delays.
Japan launched a long-term project in 2004 to expand and improve efficiency at three of its main port clusters: Tokyo-Yokohama, Nagoya-Yakkaichi and Osaka-Kobe.
Japan's top container port of Tokyo is scheduled to add three terminals with a draft of 15 to 16 metres in an effort to handle the latest generation of container ships.
Makoto Yashiki, president of Sony Supply Chain Solutions, said there was no doubt Japanese ports were “languishing”.
Data from Containerization International shows that Tokyo was ranked 23rd in the world last year while Busan was fifth.
Some observers say Japan should concentrate of on developing one port, following South Korea's example.
Recent reports said that Japan was also moving ahead with plans to privatize its port operations, starting with the country's largest port, Tokyo.
Authorities have announced that the Tokyo Metropolitan government's Port and Harbour Bureau will privatize the Tokyo Port Terminal Public Corp by April 2008, said reports.
The public corporation handles over 70% of foreign trade container throughput at the port of Tokyo.
According to Aya Yoshioka, port promotion manager at the Port and Harbour Bureau, privatization will lead to improved efficiency.
One of the main aims, said Yoshioka, would be to free the corporation from regulations from central government to allow management systems to function more freely.