Leave.EU was a separate campaign to the official Vote Leave organisation.
The Electoral Commission has referred me to the National Crime Agency under intense political pressure from anti-Brexit supporters.
Banks is the biggest donor in British political history and a co-founder of Leave.EU, a campaign group for Brexit that was fronted by Nigel Farage during the 2016 referendum campaign.
The Commission said they have reasonable grounds to suspect that Mr Banks was 'not the true source of the £8 million loans made to Better for the country'.
The Commission did not allege the money donated to the campaign came from Russian Federation.
Also under investigation are Aaron Banks, Elizabeth Bilney and other unnamed individuals.
The NCA, which is tasked with investigating serious and organised crimes, said it acted following a referral of material from the UK's Electoral Commission.
'The financial transactions we have investigated include companies incorporated in Gibraltar and the Isle of Man.
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Mr Banks welcomed the NCA investigation, saying it was an opportunity to clear up the matter.
"Our investigation has unveiled evidence that suggests criminal offences have been committed which fall beyond the remit of the Commission".
He added: "There is no evidence of any wrongdoing from the companies that I own".
"I am a United Kingdom taxpayer and I have never received any foreign donations", he said.
It went on to allege that, in fact, Mr Banks was "not the true source of the £8m loans" and the money instead came from "Rock Holdings Limited, which is incorporated in the Isle of Man".
"Any thought that the electoral commission are neutral in what they do is, I think, completely thrown out of the window by looking at the composition of the them, of the 10 people who are on that board".
Banks was the source of £2.9 million of "regulated" campaign spending (the other £5 million was from outside the key period), which is nearly 20% of the entire pro-leave spend.
The watchdog said it suspected Mr Banks, Ms Bilney and others involved in Better for the Country and Leave.EU concealed the true details of the financial transactions.
The NCA said it would not normally investigate such matters, but that the "nature" of inquiries and "potential for offences to have been committed other than under electoral law " warranted its intervention.