No ha resultado nada fácil salir a pista en Phillip Island en un primer día de entrenamientos libres protagonizados por una lluvia torrencial que terminó por encharcar zonas del circuito y forzando la cancelación, por completo, de las FP2 de MotoGP y Moto2. Los pilotos de Moto3, siendo los primeros en salir a tomar contacto con el asfalto, tuvieron una pizca más de suerte y pudieron completar ambas sesiones de entrenamientos libres. Vale, eso sí, la primera puesto que se llevó a cabo en mejores condiciones. En el aguacero australiano ha destacado por encima de todos Nicolò Bulega (SKY Racing Team VR46) con un 1’49.589, seguido de Niccolò Antonelli (Ongetta-Rivacold) y Arón Canet (Estrella Galicia).
En las condiciones más adversas John McPhee (Peugeot MC Saxoprint) y Pawi (Honda Team Asia), para variar, los que más se han atrevido aunque eventualmente Tatsuki Suzuki (CIP-Unicom Starker) se haría con la segunda plaza del malayo en la FP2.
Las peores condiciones de la FP2 impidió cualquier mejora en los tiempos.
Una hipotética segunda fila tendría a Gabriel Rodrigo (RBA Racing Team), Andrea Migno (SKY Racing Team VR46) y al propio Suzuki como protagonistas. Tras Canet, el mejor español clasificado ha sido Jorge Martin (Pull & Bear Aspar) que se coloca en la 15ª plaza a más de dos segundos y medio del tiempo de Bulega.
Resultados FP1 Moto3 Australia 2016:
| Pos. | Num. | Piloto | País | Equipo | Moto | Km/h | Tiempo | Diferencia1st/Prev. |
| 1 | 8 | Nicolo BULEGA | ITA | SKY Racing Team VR46 | KTM | 225.8 | 1'49.589 | |
| 2 | 23 | Niccolò ANTONELLI | ITA | Ongetta-Rivacold | Honda | 224.6 | 1'50.045 | 0.456 / 0.456 |
| 3 | 44 | Aron CANET | SPA | Estrella Galicia 0,0 | Honda | 224.7 | 1'50.126 | 0.537 / 0.081 |
| 4 | 19 | Gabriel RODRIGO | ARG | RBA Racing Team | KTM | 227.3 | 1'50.525 | 0.936 / 0.399 |
| 5 | 16 | Andrea MIGNO | ITA | SKY Racing Team VR46 | KTM | 221.1 | 1'51.131 | 1.542 / 0.606 |
| 6 | 24 | Tatsuki SUZUKI | JPN | CIP-Unicom Starker | Mahindra | 222.1 | 1'51.182 | 1.593 / 0.051 |
| 7 | 55 | Andrea LOCATELLI | ITA | Leopard Racing | KTM | 218.2 | 1'51.243 | 1.654 / 0.061 |
| 8 | 4 | Fabio DI GIANNANTONIO | ITA | Gresini Racing Moto3 | Honda | 221.0 | 1'51.515 | 1.926 / 0.272 |
| 9 | 64 | Bo BENDSNEYDER | NED | Red Bull KTM Ajo | KTM | 220.8 | 1'51.741 | 2.152 / 0.226 |
| 10 | 11 | Livio LOI | BEL | RW Racing GP BV | Honda | 224.9 | 1'51.746 | 2.157 / 0.005 |
| 11 | 95 | Jules DANILO | FRA | Ongetta-Rivacold | Honda | 220.9 | 1'51.824 | 2.235 / 0.078 |
| 12 | 17 | John MCPHEE | GBR | Peugeot MC Saxoprint | Peugeot | 222.9 | 1'51.848 | 2.259 / 0.024 |
| 13 | 84 | Jakub KORNFEIL | CZE | Drive M7 SIC Racing Team | Honda | 229.1 | 1'51.896 | 2.307 / 0.048 |
| 14 | 48 | Lorenzo DALLA PORTA | ITA | SKY Racing Team VR46 | KTM | 225.5 | 1'52.040 | 2.451 / 0.144 |
| 15 | 88 | Jorge MARTIN | SPA | Pull & Bear Aspar Mahindra Team | Mahindra | 222.8 | 1'52.132 | 2.543 / 0.092 |
| 16 | 33 | Enea BASTIANINI | ITA | Gresini Racing Moto3 | Honda | 220.9 | 1'52.180 | 2.591 / 0.048 |
| 17 | 58 | Juanfran GUEVARA | SPA | RBA Racing Team | KTM | 224.8 | 1'52.290 | 2.701 / 0.110 |
| 18 | 77 | Lorenzo PETRARCA | ITA | 3570 Team Italia | Mahindra | 221.3 | 1'52.304 | 2.715 / 0.014 |
| 19 | 89 | Khairul Idham PAWI | MAL | Honda Team Asia | Honda | 225.3 | 1'52.480 | 2.891 / 0.176 |
| 20 | 9 | Jorge NAVARRO | SPA | Estrella Galicia 0,0 | Honda | 222.2 | 1'52.595 | 3.006 / 0.115 |
| 21 | 20 | Fabio QUARTARARO | FRA | Leopard Racing | KTM | 221.6 | 1'52.705 | 3.116 / 0.110 |
| 22 | 41 | Brad BINDER | RSA | Red Bull KTM Ajo | KTM | 226.9 | 1'52.711 | 3.122 / 0.006 |
| 23 | 21 | Francesco BAGNAIA | ITA | Pull & Bear Aspar Mahindra Team | Mahindra | 224.0 | 1'52.960 | 3.371 / 0.249 |
| 24 | 6 | Maria HERRERA | SPA | MH6 Team | KTM | 225.0 | 1'52.997 | 3.408 / 0.037 |
| 25 | 76 | Hiroki ONO | JPN | Honda Team Asia | Honda | 224.2 | 1'53.071 | 3.482 / 0.074 |
| 26 | 40 | Darryn BINDER | RSA | Platinum Bay Real Estate | Mahindra | 230.2 | 1'53.398 | 3.809 / 0.327 |
| 27 | 36 | Joan MIR | SPA | Leopard Racing | KTM | 224.2 | 1'53.950 | 4.361 / 0.552 |
| 28 | 65 | Philipp OETTL | GER | Schedl GP Racing | KTM | 223.3 | 1'54.308 | 4.719 / 0.358 |
| 29 | 3 | Fabio SPIRANELLI | ITA | CIP-Unicom Starker | Mahindra | 219.6 | 1'54.329 | 4.740 / 0.021 |
| 30 | 42 | Marcos RAMIREZ | SPA | Platinum Bay Real Estate | Mahindra | 224.1 | 1'54.491 | 4.902 / 0.162 |
| 31 | 12 | Albert ARENAS | SPA | Peugeot MC Saxoprint | Peugeot | 217.8 | 1'55.056 | 5.467 / 0.565 |
| 32 | 43 | Stefano VALTULINI | ITA | 3570 Team Italia | Mahindra | 217.4 | 1'55.253 | 5.664 / 0.197 |
| 33 | 7 | Adam NORRODIN | MAL | Drive M7 SIC Racing Team | Honda | 219.8 | 1'56.545 | 6.956 / 1.292 |
Resultados FP2 Moto3 Australia 2016:
| Pos. | Num. | Piloto | País | Equipo | Moto | Km/h | Tiempo | Diferencia1st/Prev. |
| 1 | 17 | John MCPHEE | GBR | Peugeot MC Saxoprint | Peugeot | 219.5 | 1'54.692 | |
| 2 | 24 | Tatsuki SUZUKI | JPN | CIP-Unicom Starker | Mahindra | 217.1 | 1'55.143 | 0.451 / 0.451 |
| 3 | 89 | Khairul Idham PAWI | MAL | Honda Team Asia | Honda | 224.3 | 1'55.409 | 0.717 / 0.266 |
| 4 | 19 | Gabriel RODRIGO | ARG | RBA Racing Team | KTM | 224.0 | 1'55.517 | 0.825 / 0.108 |
| 5 | 58 | Juanfran GUEVARA | SPA | RBA Racing Team | KTM | 226.1 | 1'55.912 | 1.220 / 0.395 |
| 6 | 41 | Brad BINDER | RSA | Red Bull KTM Ajo | KTM | 228.4 | 1'55.971 | 1.279 / 0.059 |
| 7 | 23 | Niccolò ANTONELLI | ITA | Ongetta-Rivacold | Honda | 216.5 | 1'56.130 | 1.438 / 0.159 |
| 8 | 48 | Lorenzo DALLA PORTA | ITA | SKY Racing Team VR46 | KTM | 223.5 | 1'56.483 | 1.791 / 0.353 |
| 9 | 76 | Hiroki ONO | JPN | Honda Team Asia | Honda | 223.0 | 1'56.578 | 1.886 / 0.095 |
| 10 | 84 | Jakub KORNFEIL | CZE | Drive M7 SIC Racing Team | Honda | 225.3 | 1'56.604 | 1.912 / 0.026 |
| 11 | 4 | Fabio DI GIANNANTONIO | ITA | Gresini Racing Moto3 | Honda | 220.0 | 1'56.765 | 2.073 / 0.161 |
| 12 | 7 | Adam NORRODIN | MAL | Drive M7 SIC Racing Team | Honda | 216.6 | 1'56.824 | 2.132 / 0.059 |
| 13 | 64 | Bo BENDSNEYDER | NED | Red Bull KTM Ajo | KTM | 219.2 | 1'56.825 | 2.133 / 0.001 |
| 14 | 95 | Jules DANILO | FRA | Ongetta-Rivacold | Honda | 220.1 | 1'56.874 | 2.182 / 0.049 |
| 15 | 88 | Jorge MARTIN | SPA | Pull & Bear Aspar Mahindra Team | Mahindra | 219.8 | 1'56.942 | 2.250 / 0.068 |
| 16 | 8 | Nicolo BULEGA | ITA | SKY Racing Team VR46 | KTM | 222.5 | 1'56.968 | 2.276 / 0.026 |
| 17 | 11 | Livio LOI | BEL | RW Racing GP BV | Honda | 221.4 | 1'57.068 | 2.376 / 0.100 |
| 18 | 65 | Philipp OETTL | GER | Schedl GP Racing | KTM | 221.1 | 1'57.146 | 2.454 / 0.078 |
| 19 | 20 | Fabio QUARTARARO | FRA | Leopard Racing | KTM | 218.3 | 1'57.291 | 2.599 / 0.145 |
| 20 | 12 | Albert ARENAS | SPA | Peugeot MC Saxoprint | Peugeot | 215.1 | 1'57.444 | 2.752 / 0.153 |
| 21 | 55 | Andrea LOCATELLI | ITA | Leopard Racing | KTM | 216.1 | 1'57.506 | 2.814 / 0.062 |
| 22 | 21 | Francesco BAGNAIA | ITA | Pull & Bear Aspar Mahindra Team | Mahindra | 217.1 | 1'57.678 | 2.986 / 0.172 |
| 23 | 36 | Joan MIR | SPA | Leopard Racing | KTM | 224.6 | 1'58.306 | 3.614 / 0.628 |
| 24 | 16 | Andrea MIGNO | ITA | SKY Racing Team VR46 | KTM | 220.5 | 1'59.418 | 4.726 / 1.112 |
| 25 | 44 | Aron CANET | SPA | Estrella Galicia 0,0 | Honda | 216.7 | 1'59.474 | 4.782 / 0.056 |
| 26 | 42 | Marcos RAMIREZ | SPA | Platinum Bay Real Estate | Mahindra | 218.7 | 2'00.444 | 5.752 / 0.970 |
| 27 | 3 | Fabio SPIRANELLI | ITA | CIP-Unicom Starker | Mahindra | 221.1 | 2'00.590 | 5.898 / 0.146 |
| 28 | 6 | Maria HERRERA | SPA | MH6 Team | KTM | 218.9 | 2'00.969 | 6.277 / 0.379 |
| 29 | 33 | Enea BASTIANINI | ITA | Gresini Racing Moto3 | Honda | 215.3 | 2'00.979 | 6.287 / 0.010 |
| 30 | 14 | Matt BARTON | AUS | Suus Honda | FTR Honda | 205.2 | 2'02.351 | 7.659 / 1.372 |