| Part 1 (comprising sections 2 to 7 | General preliminary provisions. |
| Part 2 (comprising sections 8 to 10 | Purpose and principles of Act. |
| Part 3 (comprising sections 11 to 16 | Sustainability measures. |
| Part 9 (comprising sections 174 to 186) | Taiapure-local fisheries and customary fisheries. |
| Sections 187 to 190 | Weights, conversion factors, records, and returns, etc |
| Part 14 (comprising sections 261 to 275 | Cost recovery. |
| Sections 276 to 282 | National Fisheries Advisory Council. |
| Sections 294 to 296 | Administration generally. |
| Sections 297 to 311 | Miscellaneous provisions (including regulation-making powers, protection of the Crown, southern scallop enhancement programmes). |
| Section 314(1)(h), (i), (o), (p), (s), (ze), (zk), and (zm) | Repeal of various provisions of Fisheries Act 1983. |
| Sections 316 to 318 | Amendments to other Acts and regulations. |
| Section 322 | Relationship between offence provisions of Fisheries Act 1983 and Fisheries Act 1986. |
| Section 324 | Savings relating to rock lobster regulations. |
| Section 327 | Savings related to commodity levy orders. |
| Section 329 | Validation of certain decisions relating to permits. |
| Section 330 | Certain fishing restrictions may affect quota management areas. |
| Section 334 | Conversion of transferable term quota (rock lobster). |
| Section 335 | Savings relating to quota appeals. |
| Section 353 | Statutory debts under Fisheries Act 1983. |
| Section 360 | Provisions relating to taiapure-local fisheries. |
| Section 361 | Transitional offences and penalties. |
| Section 365 | Transitional provision relating to cost recovery. |
| Section 366 | Southern scallop enhancement programme. |
| Section 367 | Allocation of jack mackerel quota. |
| Section 368 | Nelson-Marlborough dredge oyster quota. |
| Section 370 | Transitional provision relating to performance of functions by outside agencies. |
| Schedule 1 | Fishery management and quota management areas defined. |
| Schedule 2 | Stocks whose abundance is highly variable. |
| Schedule 3 | Stocks managed with an alternative total allowable catch. |
| Schedule 9, Parts 1, 2, and 3 | Allocation of quota for jack mackerel, Nelson-Marlborough dredge oysters, and Northland scallops. |
| Schedule 10 | Levies. |
| Schedule 12, Parts 1, II, 3, and 7 | Certain amendments to other Acts. |