Rob Wainwright, the director of the agency, has called on regulators and industry leaders to work together in order to tackle an increasingly common problem.
He told 'Panorama': "It's growing quite quickly and we're quite concerned."
Cryptocurrencies have garnered lots of headlines over recent months, in large part due to the success of bitcoin, which is the best known of the digital currencies.
Unlike with traditional currencies, such as the pound or the euro, cryptocurrencies are not printed by governments and traditional banks, and nor are they regulated by them.
As a result, they are considered to be more vulnerable to illegal activities.
Mr Wainwright explained: "They're not banks and governed by a central authority so the police cannot monitor those transactions.
"And if they do identify them as criminal they have no way to freeze the assets unlike in the regular banking system."
Mr Wainwright added that the people running the bitcoin industries have a responsibility to work with the relevant authorities in order to get a hold on the problem.
He said: "They have to take a responsible action and collaborate with us when we are investigating very large-scale crime.
"I think they also have to develop a better sense of responsibility around how they're running virtual currency."
Meanwhile, Alison McGovern, Labour MP for Wirral South, has called for an enquiry into cryptocurrencies.
She said: "I think that will draw the attention of the Treasury and the Bank [of England] and others to how we put in place a regulatory system.
"I think probably hand on heart we have all been too slow, but the opportunity is not lost, and we should all get on with the job now."