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The list of ship commissionings in 1999 includes a chronological list of all ships commissioned in 1999.
| Operator | Ship | Flag | Class and type | Pennant | Other notes | |
|---|---|---|---|---|---|---|
| 20 March |  United States Navy | Porter | Arleigh Burke-class destroyer | DDG-78 | ||
| 24 April | United States Navy | Higgins | Arleigh Burke-class destroyer | DDG-76 | ||
| 2 June |  Indian Navy | Mysore | Delhi-class destroyer | D60 | ||
| 5 June |  Royal Canadian Navy | Brandon | Kingston-class coastal defence vessel | MM 710 | ||
| 6 June |  French Navy | Aconit | La Fayette-class frigate | F713 | ||
| 10 July |  Royal Australian Navy | Waller | Collins-class submarine | SSG 75 | ||
| 18 July | Royal Canadian Navy | Summerside | Kingston-class coastal defence vessel | MM 711 | ||
| 25 September |  Royal Navy | Grimsby | Sandown-class minehunter | M108 | ||
| 23 October | United States Navy | O'Kane | Arleigh Burke-class destroyer | DDG-77 | ||
| 10 November |  Royal Malaysian Navy | Jebat | Lekiu-class frigate | F29 | ||
| 27 November | Royal Navy | Vengeance | Vanguard-class submarine | S31 | ||
| 10 December |  Royal New Zealand Navy | Te Mana | Anzac-class frigate | F111 | ||
| 23 December | French Navy | Téméraire | Triomphant-class submarine | S617 |