(D)：Difending Champion
| Date | Championships | Course | Venue | Champion | |
| 4/22 – 4/25 | Asian Tour Kirin Open Golf Championship | Ibaraki Golf Club East Course | IBARAKI | Kyoung-Ju Choi | |
| 6/24 – 6/27 |  |
32nd 1999 Japan Women’s Open Golf Championship | Kasumigaseki Country Club East Course | SAITAMA | Mayumi Murai |
| 7/13 – 7/16 | 84th 1999 Japan Amateur Golf Championship | Sodegaura Country Club Sodegaura Course | CHIBA | Hidemasa Hoshino | |
| 8/18 – 8/20 | 5th 1999 Japan Junior Golf Championship Boy’s 15-17 Division | Kasumigaseki Country Club East Course | SAITAMA | Yukinobu Watanabe | |
| 8/19 – 8/20 | 5th 1999 Japan Junior Golf Championship Boy’s 12-14 Division | Kasumigaseki Country Club East Course | SAITAMA | Fumio Matsumoto | |
| 8/19 – 8/20 | 5th 1999 Japan Junior Golf Championship Girl’s 15-17 Division | Kasumigaseki Country Club West Course | SAITAMA | Hijiri Takamatsu | |
| 8/19 – 8/20 | 5th 1999 Japan Junior Golf Championship Girl’s 12-14 Division | Kasumigaseki Country Club West Course | SAITAMA | Sakura Yokomine | |
| 8/24 – 8/27 | 53rd 1999 Japan Collegiate Golf Championship | Aigi Country Club East/Center Course | GIFU | Naomi Ota | |
| 8/25 – 8/27 | 36th 1999 Japan Women’s Collegiate Golf Championship | Aigi Country Club East/Center Course | GIFU | Shiho Oyama | |
| 9/30 – 10/3 | |
64th 1999 Japan Open Golf Championship | Otaru Country Club New Course | HOKKAIDO | Naomichi Ozaki |
| 10/6 – 10/8 | 41st 1999 Japan Women’s Amateur Golf Championship | Minami Aichi Country Club | AICHI | Yun-Jye Wei | |
| 10/6 – 10/8 | 21st 1999 Japan Senior Golf Championship | Beppu Golf Club Tsurumi Course | OITA | Makiei Bito | |
| 10/14 – 10/17 | |
9th 1999 Japan Senior Open Golf Championship | Rokkokokusai Golf Club East/Center Course | HYOGO | Graham Marsh |
| 10/21 – 10/22 | 6th 1999 Japan Mid-Senior Golf Championship | Miyazaki Country Club | MIYAZAKI | Teruyuki Nishimoto | |
| 10/21 – 10/22 | 6th 1999 Japan Grand-Senior Golf Championship | Miyazaki Country Club | MIYAZAKI | Kinji Ando | |
| 10/21 – 10/22 | 7th 1999 Japan Women’s Senior Golf Championship | Takarazuka Golf Club Old Course | HYOGO | Yukiko Oita | |
| 10/26 – 10/29 | 8th 1999 Japan Amateur Match Play Golf Championship | Aichi Country Club | AICHI | Tomohiro Kondo | |
| 10/26 – 10/29 | 8th 1999 Japan Women’s Amateur Match Play Golf Championship | Aichi Country Club | AICHI | Shiho Oyama | |
| 11/10 – 11/12 | 4th 1999 Japan Mid-Amateur Golf Championship | Kurashiki Country Club | OKAYAMA | Tetsuo Sakata | |
| 11/18 – 11/19 | 4th 1999 Japan Women’s Mid-Amateur Golf Championship | Sobu Country Club Imba Course | CHIBA | Kaoru Ninomiya | |