The 1999 Japan Open Tennis Championships was a tennis tournament played on outdoor hard courts at the Ariake Coliseum in Tokyo, Japan that was part of the International Series Gold of the 1999 ATP Tour and of Tier III of the 1999 WTA Tour. The tournament was held from April 12 through April 18, 1999. Nicolas Kiefer and Amy Frazier won the singles titles.
| Country | Player | Rank | Seed | |
|---|---|---|---|---|
 Japan | Ai Sugiyama | 27 | 1 | |
 United States | Amy Frazier | 35 | 2 | |
| United States | Corina Morariu | 36 | 3 | |
| United States | Kimberly Po | 58 | 4 | |
| Kristina Brandi | 65 | 5 | ||
| United States | Meghann Shaughnessy | 68 | 6 | |
| United States | Jane Chi | 75 | 7 | |
| Wang Shi-ting | 77 | 8 |
The following players received wildcards into the singles main draw:
The following players received wildcards into the doubles main draw:
The following players received entry from the singles qualifying draw:
The following players received entry as lucky losers:
See main article: 1999 Japan Open Tennis Championships – Men's singles. Nicolas Kiefer defeated Wayne Ferreira, 7–6(7–5), 7–5.
See main article: 1999 Japan Open Tennis Championships – Women's singles. Amy Frazier defeated Ai Sugiyama, 6–2, 6–2.
See main article: 1999 Japan Open Tennis Championships – Men's doubles. Jeff Tarango / 
Daniel Vacek defeated Wayne Black / Brian MacPhie, 4–3, retired.
See main article: 1999 Japan Open Tennis Championships – Women's doubles. Corina Morariu / Kimberly Po defeated 
Catherine Barclay / Kerry-Anne Guse, 6–3, 6–2.
