The caller accused Mr Baillieu of avoiding tough questions, and challenged him to "be a man".
But when the transcript of the airwaves encounter appeared on the taxpayer-funded website premier.vic.gov.au the criticism had vanished.
Instead, the transcript listed the question as "inaudible" - despite it being clearly understandable on recordings of the interview by the State Parliament library.
During the interview, 3AW listener Brendan phoned Neil Mitchell to say he had "one statement and one question".
"Ted, you're no different to every other premier," he said. "You only answer the questions that you want to answer.
Why can't you stand up and be a man and just say 'Yes' and 'No' and give us the real facts instead of pussyfooting and dancing around? It's just unbelievable."
Mr Baillieu's spokesman, Paul Price, said the comments had not been deliberately omitted.
Mr Price said a Government media adviser recorded the February 3 interview on a digital device at the 3AW studio but the caller's comments were not clear.
He said the recording was given to a staffer in either the Premier's office or the Department of Premier and Cabinet, to be typed into a transcript and published online, but the caller's comments were deemed "inaudible".
"We don't tamper with transcripts," he said.
"At any of the doorstops we have, the Premier is often the focus of negative commentary and that is spelled out directly in transcripts.
"This was just a function error of the audio that was taken on the day."
Mr Price also denied Mr Baillieu or any of his advisers had ordered editing of the transcript.
The premier.vic.gov.au website is Mr Baillieu's official website, which records his speeches, publishes his media releases, provides his contact details and contains transcripts of press conferences and media interviews.
Opposition Leader Daniel Andrews accused the Government of intentionally editing out all negative references to the Premier's performance from the transcript before posting it online.
"The Government doesn't have a plan to keep Victorians in work, but has found the time to doctor transcripts to protect the Premier's reputation," Mr Andrews said.
"If the Premier actually started doing some work, maybe he wouldn't be copping criticism."
It is not the first time the Government has been accused of doctoring transcripts.
Mr Andrews claimed in State Parliament last August that the Premier had removed the word "inflation" from the transcript of an ABC radio interview about the Government's wage policy that appeared on the same website.
Greens MP Greg Barber said Mr Baillieu and his Government had "selective hearing and this is only one small example".
"They spend a lot of money printing out every word from the leader that holds him up in a good light," Mr Barber said.
"But then they airbrush the leader to make him look as a guy who never puts a foot wrong."
heraldsun.com.au 19 Feb 2012
Another lies perpetuating from the mouths of politicians.
Trying not only to distort the truth but also rewriting history as to the actual events that have taken place.
Immediate dismissal should follow such fraudulent presentation of facts.