The Higher Education Funding Council for England looked into all of the cases, but either decided that no further action was required on its part or was unable to respond to the whistleblowers to follow up the complaints.
Half of the tip-offs were made anonymously.
The Hefce records for January 2010 to October 2011, released to Times Higher Education under the Freedom of Information Act, show that only four complaints were made using the formal Public Interest Disclosure Act mechanism, which protects whistleblowers who speak out against wrongdoing in the workplace.
A third of the 18 complaints related to the University of Gloucestershire in 2010.
The institution had a turbulent year as it sought to recover from a £31.6 million debt. Its vice-chancellor departed and it lost a damaging employment tribunal to one of its managers, Jan Merrigan.
Hefce audited Gloucestershire's student number returns in 2010.
The Gloucestershire complaints that were submitted to Hefce, all made anonymously, included a request "for each member of the finance team to be interviewed alone during the forthcoming Hefce data audit".
A summary of Hefce's response states: "Audit team advised. Request has not been shared with the institution to ensure that the audit is not influenced."
There was also a complaint about alleged "variance in student number reporting and tuition fee recovery". Hefce said that this had "already been prioritised" in the audit.
Another Gloucestershire complaint alleged that "staff [were] told to lie during [the] forthcoming audit". Hefce's response states: "Audit team aware of the factors which may have prompted staff concerns."
Paul Drake, Gloucestershire's executive director of external relations, said the university was "aware of a number of the issues raised by anonymous individuals, but has not been able to respond to them individually as the authors are unknown".
He noted that "some of the concerns expressed date from a turbulent period of the university's past", adding that a "change agenda" had brought about "a more stable institution and positive financial surpluses".
Other complaints submitted to Hefce concerned the alleged "manipulation of the NSS" at two unnamed institutions. Hefce found that no action was required.
One of the formal Public Interest Disclosures concerned Coventry University, where there was a claim that a "company connected with the university" was "alleged to be returning falsified enrolments".
But Hefce said that "no evidence...[was] found during the audit which was instigated" and described the allegation as "unsubstantiated".
A spokesman for the funding council said that judgements were made "in all cases as to what action was necessary, either by Hefce or the institutions involved".
He added that "if necessary, the matter was investigated to give us the information we needed".