Revisions to Finance Secretary John Swinney's draft budget show £800,000 has been moved from Scottish Water to "strategic communications" in the run-up to the referendum.
The revised spending also showed an extra £800,000 for referendum costs this year though the money has been brought forward, the Government said, leaving the overall budget for the vote at £13.7 million.
Scottish Conservative finance spokesman Gavin Brown said: "It seems Alex Salmond has taken money out of infrastructure, and put it into his pot for spinning through a referendum.
"On countless occasions the Scottish Government has failed to be straight with the Scottish people about its plans to break up the UK, and dodged almost every question asked.
"It is time for it to come clean on exactly what this hastily moved money will be spent on."
Drew Smith, Scottish Labour's constitutional spokesperson, said: "At a time when ordinary Scots are struggling to pay bills and put food on the table, it seems the sky is the limit for Alex Salmond and his referendum propaganda."
A Scottish Government spokeswoman said Scottish Water's use of short-term loans had increased funds available to ministers, which had been "deployed to support strategic communications".
She added: "There has been no change to the cost of the referendum."