The call for Kevin Pringle to give evidence to the inquiry came as the adviser was named in Leveson Inquiry documents as a contact with News Corporation representative Frederic Michel on March 2 last year.
But a spokesman for Mr Salmond hit back, claiming Labour's attack was an "embarrassing blunder" as had been shown by representations to the inquiry last Thursday asking for corrections to the documents and clarifying who was involved.
However, Labour party business manager Paul Martin said Mr Pringle was the First Minister's head of media relations "yet the Scottish Government expect us to believe he had no role in managing the media relationship which Alex Salmond prizes most highly – his relationship with Rupert Murdoch".
Mr Salmond's spokesman accused Labour of flailing around "in a bid to throw as much mud as possible".
He said: "Their claims are completely unfounded because the fact is this phone call was actually with the First Minister, and did not involve any advisers, as we made clear last Thursday."
Labour accused the SNP of cowardice yesterday after none of the party's MPs turned up to an Urgent Question in the Commons on the UK Government's dealings with the Murdoch empire.
The SNP said the party was represented by MPs from Plaid Cymru.