Police Scotland's deputy chief constable Iain Livingstone, head of crime, organised crime and counter terrorism, warned that there had been a "lack of clarity" about the NCA's remit.
He is concerned that the role of the NCA, launched last week, is unclear and that the public need to know whether the force has "primacy" north of the border.
He said: "I want to clarify the relationship between the NCA and Police Scotland.
"It has got no remit in counter terrorism in Scotland. It has got some research work on cyber crime in counter terrorism but operational responsibility for organised crime and counter terrorism in Scotland lies with Police Scotland, specifically the Scottish Crime Division.
"The NCA's role is to lead support and co-ordinate investigations in relation to serious organised crime in England and Wales but in Scotland their role is only to support."
Mr Livingstone, former assistant chief constable of Lothian and Borders Police, said Police Scotland will work with the NCA.
He said: "Our relationship with them is close but it is a very different one. It wasn't clear when they launched. There is a lot of mutual interest to work with them to protect the UK and beyond but there is a fundamental difference.
"The key constitutional point for us is the director general of the NCA has the power to direct chief constables in England and Wales in matters relating to organised crime but cannot direct the chief constable of Scotland or Northern Ireland.
"We want to work really closely with them and they have an international network of officers around the world and we will continue to utilise that and they have some specialist resources, but in terms of operational delivery on the ground, that is Police Scotland led."
He also said he was confident of Scotland's own strategies.
He said: "We already have our own organised crime strategy. We are in an advanced state to England and Wales.
"In Scotland the Police Service of Scotland has primacy for tackling organised crime and counter terrorism."
Last week when the NCA was launched arrests were made across the UK, including one in Troon, and it revealed plans to subject Britain's most notorious gangsters to 24-hour surveillance.
Gordon Meldrum, commander of organised crime for the NCA and former head of the Scottish Crime and Drug Enforcement Agency said last week drug barons and convicted organised criminals on both sides of the Scottish-English border are to be subjected to 24 hour-a-day lifelong management under the new "super Asbos".
This will include restricting travel, how much money they can carry and who they can meet.
Mr Meldrum has also praised the work of Police Scotland and suggested the rest of the UK could learn from their strategies on organised crime and counter terrorism.
He said he wants to see police "mark" the criminals for 365 days of the year.
The NCA will target the 37,000 high-level gangsters and 5500 crime groups across the UK - including approximately 3500-high level crooks in Scotland - and will work alongside Police Scotland.
The agency did not respond to requests for a comment.