The Ministry of Justice is to make a £2bn cut in its £9bn annual budget, senior officials have been told today, raising union fears that the jobs of 15,000 of the department's 80,000 staff could be at risk.

Ann Beasley, the MoJ's director-general of finance, informed senior civil servants this morning of the scale of savings expected by the Treasury and warned them that the bulk will have to be made within the first 12 to 24 months and will inevitably involve job losses.

"It will also mean there will have to be less of us," says Beasley in a letter sent to senior civil service grades today. "Over £4bn of the department's current budget is spent on staff costs and we cannot streamline the organisation to work effectively and efficiently without considering staff numbers."

It has been widely leaked that the justice secretary, Ken Clarke, has been among the first Whitehall department ministers to agree a spending reduction target with the Treasury.

While all departments have been asked to model 25% and 40% savings, it appears that the MoJ, which runs the courts and prisons in England and Wales, is among the first to agree what the actual scale of the share of the cuts will be.

The Public and Commercial Services Union said the MoJ letter was the first indication of the scale of savings to be demanded by the coalition government and implied job cuts on an unprecedented scale.

The Whitehall union said more than £4bn of the MoJ's £9bn budget was fixed for legal aid and for the running costs of prisons and so cuts on this scale could not be delivered without closing prisons or bringing courts to a standstill. "We also fear almost 15,000 of the MoJ's 80,000 staff could be at risk of losing their jobs," said a PCS spokesman.

Mark Serwotka, the PCS general-secretary, said: "This paints a devastating picture of the true scale of the cuts being imposed upon departments by this coalition government. We'll take every opportunity to remind the government and the public that there is an alternative and that these politically-motivated cuts are entirely avoidable."

The MoJ letter confirms that Clarke has already held a "bilateral" meeting with the chief secretary to the Treasury, Danny Alexander, but says that formal negotiations are continuing on the basis of their "first high-level" MoJ submission to the Treasury, which went in on 16 July.

The MoJ director-general of finance said that during August and early September "teams will be working with colleagues in the businesses" to develop more detailed proposals to firm up their Treasury bid before it is agreed and announced on 20 October. It is expected to set out the cuts to be made over the next four years.

"I cannot give you more information at the moment about our bid as we are in negotiations with HM Treasury. I can, however, tell you that the scale of the savings we have to make are extremely challenging and, given our current budget of around £9bn, are expected to be around £2bn.

"The level of savings we expect to have to make from our headquarters and administrative areas alone is around £450m – around one-third of our current administrative costs. This is in line with the one-third savings required by the government."

Beasley says that "many savings will have to be made quickly within the first 12-24 months" and efficiencies alone will not be enough. "It will mean we have to look at every opportunity to work differently and better. It will also mean there will have to be less of us."

She tells senior managers that it is important they listen to staff concerns and be honest about "what we do and don't know" and when they can be told more. "In doing this, we must keep secure the details of our bid to HM Treasury so we do not compromise our negotiations or attract premature speculation."

The Treasury bid includes both proposed savings and "pressures that we consider will continue" into the 2010 comprehensive spending review period which runs up until 2014.

A separate message to staff circulated today on the MoJ's intranet omits the key figures indicating the scale of the cuts.

The PCS union says the £2bn of savings to be found is equivalent to the entire budget for prisons, or the money the department spends each year on courts and tribunals.

A justice ministry spokesman said: "The Ministry of Justice has submitted proposals for savings to HM Treasury. Like all departments we were asked to plan for savings of 25% and 40% as part of the coalition government's deficit reduction plan.

"We are discussing options with the treasury and will not provide a running commentary on the process. No decisions have been made. The outcome of the spending eeview will be announced on 20 October."