The offer was rejected as it would have been outweighed by longer working hours and a cuts in expenses, mileage allowances and overtime rates, unions said.
Unions, including Prospect, the GMB and the FDA, all voted between Friday last week and Monday - to reject the offer, while PCS – the UK’s largest civil service trade union – is still balloting members.
The five-year pay offer included a 3% rise in the first three years, followed by 1% rises in years four and five.
FDA national officer Victoria Taylor, who negotiates on behalf of MoJ members, said: “FDA members in the MoJ have been clear that the offer on the table is not good enough.
“They are not prepared to tie themselves to a five-year deal that demands they work extra hours, face a reduction in their terms and conditions and, in some cases, a significant real terms pay cut.
“The proposed offer is extremely complicated but it is clear that staff can see it for what it is – robbing Peter to pay Paul.”
The five-year pay offer was also rejected as it failed to offer a guaranteed above inflation increase over the period it would cover.
The so-called Modernising the Employment Proposition offered by the MoJ put forward increasing weekly working hours for members from between 35-37 hours to 38 hours.
Overtime pay would be reduced to a flat single time rate while overnight stay allowances would be cut from £23 to £9.
Other changes included replacing the London allowance with non-pensionable payment of £500 in the third year of the deal, followed by £1,000 in years four and five. Sick pay periods would also be shortened.
Negotiator for Prospect union Brian Harris said: “During the negotiations, Prospect raised a number of concerns about the length of the deal, the allowances that were being removed, flat-rate overtime and other significant changes to staff contracts.
“We will be going back to the MoJ to discuss the next steps after our members made such a clear decision to reject the offer.”
GMB national officer George Georgiou called the offer a “retrograde step in terms of pay, conditions and working hours”.
PCS will decide on 30 August whether to accept or reject the offer after its ballot closes.
In July, the government said it had agreed a pay deal for teachers, soldiers and prison officers.
This followed a 6.5% pay deal for NHS staff in June.
