Deny does not mean the same as rebut (which means argue to the contrary, producing evidence), or refute (which means to win such an argument).
See this (Big names in sleaze story; Hindustan Times; June 25, 2006):
"If there was pressure, Singh may have escaped arrest. All the accused have already been sent to judicial custody," stated SSP Dehra Dun SK Gunjyal refuting charges of political pressure on the police.
Gunjyal did not refute anything, he merely denied charges of political pressure. He did not even rebut the accusation.
Another example (TN police refute Jayalalithaa's charges; The Hindu; May 27, 2006):
Refuting AIADMK supremo Jayalalitha's charge that she was being provided with inadequate security, the Tamil Nadu police today defended itself by saying that she was being provided with "Z+" category security as per the National Security Guard rules.
All the Tamil Nadu police did was to rebut the allegation.
Rebut and refute are not synonyms for deny. Rebut means to argue to the contrary, producing evidence; to refute is to win such an argument. Neither should be used as a synonym of reject or deny, both of which are good, straightforward words. Nor should they be used for dispute or respond to.
An example of correct usage of refute (Rahul Mahajan arrested under Narcotic Act, may face long haul; Daily News & Analysis; June 5, 2006):
Police confronted Mahajan with all this evidence at Apollo hospital in the afternoon. A source said Mahajan could not refute any of the charges.
Of course, Mahajan couldn't.
But, here's another example where the reporter/sub probably meant contend (Hmar women again refute HRA stand; The Sangai Express; June 19, 2006):
The rape allegation of Hmar women at Tipaimukh sub-division appears to be taking another twist as Human Rights Alert and Hmar Women Association, both a party in investigating the incident continuing to refute each others' claims.