The planned "British FBI" could lead to political interference in policing, the Police Federation has warned.
Police that join Soca are due to become civilian staff
The Serious Organised Crime Agency (Soca) is due to absorb around 1,800 officers, plus immigration and customs officials, into its ranks in 2006.
Soca's staff will be civilian, but with powers of investigation and arrest.
Federation chairman Jan Berry said the government seemed "obsessed" with removing "the political independence to uphold the law impartially".
While the home secretary has overall responsibility for the police, chief constables currently handle operational decision-making for each force, overseen by police authorities.
A federation spokesman said: "Once you remove the office of constable from those officers that transfer to Soca, you remove the political independence that police officers hold.
"If they are agency staff, and the government has a certain agenda and puts pressure on the director general of Soca to implement that agenda, as staff they will just be told what to do."
He added: "We are fearful this is the first step towards political interference and control of policing in this country."
The Police Federation represents all rank and file officers in England and Wales.
In contrast to those officers, Soca staff will also not swear allegiance to the Queen.
Mrs Berry said: "Since the police service began, officers have sworn an allegiance to the Crown - an oath that my members take very seriously.
"But the government seems obsessed in taking this away, and with it the political independence to uphold the law impartially."
A Home Office spokesman said: "The status of Soca staff will be every bit as high as police officers, and it is not the case that Soca staff will be government employees in the way the Police Federation is suggesting.
"They will be politically neutral and accountable, as police officers are, with all the necessary police powers to do their job effectively."
Plans for Soca were unveiled last month in the Serious Organised Crime and Police Bill.
The body, of around 5,000 staff, will spearhead efforts against organised criminal gangs, which make an estimated £40bn a year in the UK.