Scottish ministers have reassured police there will be no political interference in operational matters.
The SOCA is to target drug trafficking
The pledge comes after the announcement of plans to set up the new UK-wide Serious and Organised Crime Agency (SOCA).
It will work alongside Scotland's eight forces and the Drug Enforcement Agency.
Ministers want reserve powers to direct chief constables - but Scottish Police Federation spokesman Doug Keil said that is unacceptable.
The federation said it was "hugely concerned" at what it claimed were proposals for increased ministerial powers over police.
Mr Keil said the legislation was being rushed through Holyrood in the form of a Sewel motion - the procedure by which MSPs agree to Westminster legislating on devolved matters.
However, the Scottish Executive moved to mollify the police, saying the federation's fears were unfounded.
The new body will specialise in tackling drug trafficking, people smuggling and fraud.
In Scotland, it will combine the role of the National Criminal Intelligence Service, the organised crime section of the immigration service and the serious drug trafficking arm of Customs and Excise.
The federation has written to all MSPs, Scottish MPs, and peers detailing its concerns over the proposals and the use of the Sewel procedure in putting it on to the statute book.
Mr Keil told BBC Scotland the proposals amounted to "creeping politicisation" of the police.
"I think this bill to some extent has been rushed," he said.
"I don't think there has been serious public or political debate in Scotland about these issues, which is extremely important for how serious and organised crime is dealt with.
We believe this will encroach on the political impartiality of the police
Doug Keil, Scottish Police Federation
"I would really like our politicians to study the bill carefully and make sure that the principle of operational autonomy for chief constables, and political impartiality of the police, is upheld.''
The federation argues that the bill proposes "significant new roles and powers" for the home secretary, Scottish ministers, and the director of the agency, he said.
"We believe this will encroach on the political impartiality of the police, the operation independence of chief constables, and significantly alter the tripartite structure of control and accountability which are cornerstones of our democratic constitution," he added.
While police had the legal status of "constables", the new agency would have agents.
The federation spokesman said: "We fail to understand why SOCA should set up as a non-police agency employing agents as opposed to police officers and not as a police organisation.
"SOCA will deal with crime and crime is a police business, and not something to be dealt with by an agency established, controlled and directed by the secretary of state or any other politician."
But the executive defended the plan and the use of the Sewel procedure, one of whose functions, said a spokeswoman, was to make the framing of UK-wide legislation more effective.
She added: "Nothing in the bill changes the responsibilities of Scottish forces or the SDEA, nor will affect existing tripartite policing arrangements in Scotland.
"The bill makes clear that SOCA agents can only operate in Scotland with the agreement of Scottish ministers and the director of the SDEA or a chief officer nominated by him."
SOCA agents would have to work under the direction of the Lord Advocate and procurators fiscal.
Home Office ministers had also pledged to ensure SOCA agents will only be allowed to operate north of the border after being trained and accredited, including training on the Scottish criminal justice system.
Of the claim of political interference, she said: "We have been able to ensure no UK minister can direct Scottish police forces.
"Only Scottish ministers would be able to exercise this power - and we would only envisage this being done in full consultation with the relevant police forces, ACPOS and SOCA, and in rare, extremely specific circumstances.
''For example, if forces and SOCA were unable to agree on providing each other with support on a particular operation."
In such a case, she said, Scottish ministers would act as impartial arbiters to ensure forces and SOCA were able to continue working effectively.