This is a 189% increase on the 1,293 calls to the helpline in the same period three years earlier (June 2008-May 2009) and a 276% increase on the 994 calls made in the same period four years earlier (June 2007-May 2008), according to information obtained under the Freedom of Information act by corporate investigation group Kroll.
Out of the calls received, 19% were malicious allegations made intentionally to get revenge on an individual or company, it was claimed.
Carol Sergeant, who chairs the whistleblowing charity Public Concern at Work, said: "The increase in whistleblowing reports to the FSA is both good news and bad news.
"It is encouraging that more people are now prepared to raise concerns about malpractice but it is very disappointing that they feel the only way to get their concern addressed properly is to go the regulator."
Sergeant added: "This should be a real worry to the financial services industry."
Benedict Hamilton, a managing director at Kroll, said: "Whistleblowing cases are becoming much more common and they can be hugely significant for companies; we have investigated cases where losses of up to £1 billion have been reported by a whistleblower.
"As companies increasingly invest in often risky emerging markets and individuals see criminal opportunities made possible by the advancement of technology, we believe cases of whistleblowing will continue to rise."
Hamilton added: "The increase in these cases is also being driven by the introduction of more stringent regulation and guidance governing whistleblowing procedures."
The Enterprise and Regulatory Reform Bill going through Parliament and is set for its second reading on the 14 November is set to change the UK's whistleblowing legislation.