Tongue arrived in Perth last week ahead of England's three-match ODI and five-game T20 series, but sat out their 92-run one-day warm-up win over Western Australia on Saturday.
"Josh Tongue has been ruled out of the white-ball tour of Australia due to a left big toe injury," team officials said.
"Tongue will return to the UK to undergo further assessment."
Batsman Jacob Bethell, who is returning from knee surgery, also missed the game, where Jofra Archer and Adil Rashid excelled.
Pace spearhead Archer took 3-34 and spinner Rashid 4-35 as Western Australia were bowled out for 159, having been set 252 to win.
Ben Duckett cracked 59 and Liam Dawson an unbeaten 44 for England, who open the ODI leg of the tour in Perth on Friday before the series moves to Adelaide and Hobart.
It is England's first time back in Australia since being crushed 4-1 in the 2025-26 Ashes Test series.