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The Fisheries Research Agency (FRA), an incorporated administrative agency, was established in 2001 as an independent body by incorporating nine National Fisheries Research Institutes. In 2003 it took over the duties of the Japan Marine Fishery Research Centre, and the Japan Sea-Farming Association, and, in 2006, the National Salmon Resources Centre. The FRA is responsible for research into many aspects of capture and aquaculture as well as monitoring fishing stocks. In 2009, following a request from the Fisheries Agency, it published "The Grand Design of Fisheries and Resources Management in Japan".

In 2012 the FRA (Fisheries Research Agency) assessed 52 species and 84 fishing stocks and estimated that resource levels were low for 35 stocks, medium for 34, and high for 15. Management of resources is based on several measures, including fishing rights and permits, as well as voluntary resource management supported by the Government.

Fishery rights and permits for fishing may be granted as follows:
• Fishery rights granted by prefectural governors for coastal fishing based on the fishing ground plan which sets out the type of fishery, the fishing ground and other details. The rights include operation of large-scale set-net fishing, aquaculture in specified areas, and small-scale common fishing;
• The prefectural governors may grant permits for small- to medium-scale fishing based on prefectural regulations which must be approved by MAFF; and
• MAFF may grant permits for large-scale off-shore and distant-water fishing as well as specified fishing methods for certain species. The permits may be: (i) for some designated fisheries where the total number of vessels by tonnage class and each area of operation are specified in a 5-yearly (generally) notification made by the Minister; (ii) for some specified fisheries where the Ministers grants a permit each year; or (iii) for some activities and species where notification must be made to the Minister before the start of the operation period.

TAC (Total allowance catch) are set for seven species by the Fisheries Agency based on estimates of allowable biological catch and other factors and in consultation with different stakeholders. It has been noted that, in some cases, the TAC had been greater than the allowable biological catch and Japan has not introduced an explicit ban on discards. According to the authorities, efforts have been made to ensure that the TAC conforms to the allowable biological catch and individual quota systems have been introduced for three species, including Atlantic bluefin tuna and southern bluefin tuna.

In 2011, a new resource-management framework for both capture and aquaculture was introduced under which the fishery organizations prepare and implement resource-management plans in line with the guidelines developed by the central government or prefectural authorities. As at end March 2013, 1,705 resource-management plans had been prepared.

Several measures have been taken to prevent and deter illegal, unreported, and unregulated (IUU) fishing, through bilateral cooperation and information-sharing efforts, and through regional fisheries' management organizations, for example vessel-monitoring systems and trade-related measures such as statistical document programmes and catch documentation systems.

Japan is a member of a number of international and regional fishery organizations [50]

[50] Indian Ocean Tuna Commission (IOTC), Western and Central Pacific Fisheries Commission (WCPFC), Inter-American Tropical Tuna Commission (IATTC), International Commission for the Conservation of Atlantic Tuna (ICCAT), Commission for the Conservation of Southern Bluefin Tuna (CCSBT), General Fisheries Commission for the Mediterranean (GFCM), South East Atlantic Fishery Organization (SEAFO), Convention on the Conservation and Management of Pollock Resources in the Central Bering Sea (CCBSP), North Pacific Anadromous Fish Commission (NPAFC), Commission for the Conservation of Antarctic Marine Living Resources, and Northwest Atlantic Fisheries Organization (NAFO).

According to the OECD: "General services account for nearly half of government financial transfers, of which construction of public infrastructure is the most significant." Cost reducing transfers represent only a small proportion of total support and "an interest subsidy is the major cost-reducing transfer in Japan" while "support for renewal of small fishing boats and equipment is provided to improve workers' safety at sea on family-owned coastal boats" (Table 4.17).

Table 4.17 Government transfers to fishing, 2005-11
(¥ billion)
2005 2006 2007 2008 2009 2010 2011
Decommissioning of vessels and licences 1.7 1.5 1.5 1.4 1.6 1.2 0.5

Supplementary budgets provided additional assistance in response to the 2011 earthquake. The FY2013 budget and supplementary budget provided a total of ¥48.4 billion in financial support to fishermen and cooperatives out of a total of ¥293.3 billion.