The TES Scotland had reported "informed sources" close to the Scottish Executive who suggested the universities' representations were "self-defeating".
"The 'informed sources' are very badly informed sources," David Caldwell, director of Universities Scotland, contends.
Writing in this week's issue, Mr Caldwell says the situation in England "was never the determining factor" in making the case for additional funding in Scotland, and his organisation is not claiming higher education is automatically entitled to extra cash.
He insists that the universities had made "a carefully reasoned case" in setting out the arguments for additional cash, which were based on the needs of the Scottish universities and the support they required to meet the policies of the Executive.
Mr Caldwell also takes issue with criticism from the further education sector which has argued that the universities are "jumping the gun" in demanding extra resources six years before any changes are required to deal with the English situation.
Extra funding is already flowing to English universities from the 2002 spending review, he writes, and additional income from top-up tuition fees will start in 2006 - in two years' time, not six.
Mr Caldwell describes such a view from FE as "troubling" since it suggests the colleges are lobbying against the universities. "The HE sector has welcomed the substantial increases in spending on FE in recent years and has never argued that they were undeserved," he says.
Such an attitude among the colleges would put at risk the trust between FE and HE, particularly if it was based on inaccurate and incomplete information.
"It is absurd for your source to apply the word 'self-defeating' to the presentation of a reasoned case," Mr Caldwell concludes. "What deserves to be self-defeating is your source's distortion and misrepresentation of that case."
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