Stephen House, 54, who is currently Chief Constable at the soon to be disbanded Strathclyde force, said yesterday "many, many hundreds" of support posts could be lost.
For the first time, Mr House acknowledged total job losses could reach 3000 after fears were raised by the Unison union.
Bringing together Scotland's eight forces from April 1, 2013, is projected to save the public purse £1.7 billion over 15 years.
However, while the Scottish Government pledged there would be no compulsory redundancies, concerns were raised over the scale of the cuts.
Mr House, who left his post as Assistant Commissioner at the Metropolitan Police for Strathclyde in 2007 and will command a £208,000-a-year salary in his new post, said: "It's difficult to be precise at this moment in time because calculations are still being made and it depends on a lot of different factors.
"The Government has said, and I think it's quite right, that we're not keen on the idea of compulsory redundancies, so we would be looking to identify jobs where there was some duplication, where we didn't need to do that work any more, and either redeploy those staff into other jobs or see if they wanted to take a voluntary redundancy package or early retirement. So, it's something that will be done in a co-operative and compliant way, working with the unions representing the workers."
Gerry Crawley, Unison's lead officer for police in Scotland, said: "The problem is the Scottish Government's arbitrary target to maintain police officer numbers at 17,234.
"This, combined with their failure to fund a balanced police service, means that massive cuts will fall on police support staff –whose skills and qualifications are vital to effective policing across Scotland."
Colin Steele, general secretary of the Scottish Police Federation, said: "The brutal reality is that there is monstrous duplication and waste across all of the police forces at this moment in time and anything that can be done to save money in the service can only be a good thing.
"It is the post that will be made redundant, not the person, and if the post is no longer required, then the service is making the right decision."
He added: "If the choice is getting rid of waste and repetition or cutting budgets, then it's not really a difficult choice.
"There is an obligation on the Chief Constable to deliver an efficient and effective police force."
A Scottish Government spokesman said: "We have protected, and will continue to protect, frontline police numbers, and the 1000 extra officers we have delivered have helped reduce crime to a 37-year low, while the fear of crime is also falling. We have also given a commitment to no com-pulsory redundancies among police support staff."
Scottish Labour MSP Lewis Macdonald said "the SNP's hidden agenda has been cruelly exposed". He added: "Three thousand fewer civilians in Scotland's police service will more than cancel out the benefits of 1000 police officers, if what com- munities get is simply backroom bobbies doing civilian jobs."
Scottish LibDem leader Willie Rennie said: "The SNP promised that police centralisation would protect, not cut, jobs.
"Civilian staff play an absolutely vital role in the police service. The work they do – as intelligence analysts, custody officers and community wardens – allows our police officers to spend the maximum time possible out on the beat."
Scottish Conservative justice spokesman David McLetchie said he hoped Mr House would be interviewed by Parliament "to ascertain how he intends to achieve savings of this magnitude over that period of time".