It will also investigate claims about money contained in an Isle of Man bank account.
It is understood the PSNI asked the NCA to take the lead because of the complexity and scale of the investigation.
It is the NCA's first major investigation since it began operating in Northern Ireland in May.
Investigators from the agency are expected to meet the PSNI shortly.
In a statement on Thursday, the NCA, the UK equivalent of the FBI, confirmed it had agreed to investigate the sale of Northern Ireland assets owned by the Republic of Ireland's National Assets Management Agency (Nama).
NCA deputy director of operations Graham Gardner said: "The NCA has considered a request from [the] PSNI and has agreed to lead an investigation, calling on support as necessary from PSNI officers.
BBC News NI Home Affairs Correspondent Vincent Kearney
This takes the investigation to a new level.
The NCA has a level of expertise and resources not available to the PSNI.
They include a specialist economic crime unit and a financial intelligence unit.
Those units contain specialist investigators like forensic accountants and technical experts.
The NCA also has an international reach and works with other agencies throughout the world, including Interpol, whose members include the Republic of Ireland and the United States.
"We will not be providing a running commentary on our progress but will provide updates as and when appropriate."
Earlier, an Irish parliament (Dáil) committee was told a former Nama adviser was in line for a £5m payment after the sale of Nama's property loan portfolio in Northern Ireland.
US investment firm, Pimco, pulled out of the tender bidding process after discovering the fee arrangement to Nama's former adviser, Frank Cushnahan.
The revelation came during a hearing of the Public Accounts Committee (PAC).
It is examining Nama's sale of its 850-property NI portfolio last year.
The National Assets Management Agency (Nama) is the Republic of Ireland's "bad bank", set up to deal with toxic loans during the Irish banking crisis, and the sale of Nama's Northern Ireland portfolio is known as Project Eagle.
The National Crime Agency (NCA), is to lead the investigation into the sale of Nama's NI property portfolio.