Labour said the idea would sound the death knell for the government's "levelling-up" agenda by widening the regional income gap.
The Tory leadership frontrunner presented her plan as a “war on Whitehall waste" that would also see civil service holiday entitlements slashed.
But she was forced to admit that she would have to replace national pay settlements with regional awards for all public sector workers over a period of many years.
The foreign secretary's proposal for regional pay boards to set wages in line with the local cost of living sparked fury among unions.
In a warning of confrontation with Whitehall, if she succeeds Boris Johnson on 5 September, the PCS civil service union said she could expect "opposition every step of the way".
And Labour accused her of "declaring war on herself with her fantasy recipe for levelling down".
Deputy leader Angela Rayner said Ms Truss's plans would result in "a race to the bottom on public sector workers' pay and rights".
Ms Rayner warned: "Her 'tailored' pay plans would level down the pay of northerners, worsening the divide that already exists. This out-of-touch government's commitment to levelling up is dead."
The row came as Ms Truss's campaign to seize 10 Downing Street won a major boost with the endorsement of third-placed candidate Penny Mordaunt.
And a poll by Redfield & Wilton Strategies suggested she could beat Sir Keir Starmer in a general election, with 37 per cent opting for Ms Truss as best PM against 36 per cent for the Labour leader. Faced with a choice between Rishi Sunak and Sir Keir, those questioned split 40-33 in favour of Sir Keir.
Ms Truss initially promised to save up to £8.8bn annually by "adjusting" officials' salaries to match living costs in the areas where they work.
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