It follows reports that a DTI civil servant has been disciplined after sending out an email to another Whitehall colleague requesting "background/dirt" on Channel 4 comedian Mark Thomas.
But a spokeswoman for the DTI said there was no question of a smear campaign and said the minister had made a "purely procedural request" for background information on Mr Thomas.
The emails were sent between Whitehall officials while Mr Thomas was preparing programmes last year looking at the DTI's export credit guarantee department (ECGD).
The programme was looking in particular at the DTI's support for companies hoping for a role in the construction of the controversial Ilisu dam in Turkey.
His Channel 4 show The Mark Thomas Product specialises in exposing hypocrisy and wrong-doing in high places with a mix of comedy, stunts and investigative journalism.
Alongside the request for "background/dirt" on the comedian, the memos variously describe him as "an out-and-out nutter" and a "prat".
The memos were obtained through the Data Protection Act.
Mr Thomas, speaking on BBC Radio 4's Today programme, said the affair highlighted the lack of transparency in British government.
He said such information should be automatically available to the public through a more robust Freedom of Information Act.
'Badge of honour'
Mr Thomas said he was not surprised at the nature of the memos and regarded them as a "badge of honour".
"But I think the thing here is that for a government that said it's important to be whiter than white and to be seen to be whiter than white, this is another example of them not being transparent.
"Frankly they are failing the Daz doorstep challenge on the whiter-than-whiteness bit.
"The government are there because we elected them, they are there to do our work for us, they are our documents and we should be able to see them."
But a DTI spokeswoman denied claims that Mr Caborn was digging for dirt.
She said the minister had made a "purely procedural request" for background information on Mr Thomas because of his programme's continued interest in ECGB.
"At no time did the minister make a request for 'dirt' on Mark Thomas, or ask for information to rubbish him or his programme.
"The minister was not aware of the content of the email and once the contents of the email came to light the official concerned received a warning."
'Intolerable'
The Liberal Democrats are demanding an explanation of the incident from Mr Caborn.
Trade and industry spokesman Vince Cable said: "If the reports are true, and the press officers involved were acting under ministerial instructions, then this is a very serious matter indeed.
"Such a deliberate and calculated attempt to induce civil servants to undermine a journalist for political purposes would be intolerable."
Mr Thomas has previously investigated issues including arms exports, oppression by the Indonesian armed forces and security of nuclear waste shipments.