The Referenda On The Islands group (ROTI) petitioned the Scottish Parliament to allow islanders to vote on their own constitutional future a week after the independence referendum on September 18.
But in a written submission to Holyrood's petitions committee, ministers said: "The Scottish Government is clear that Shetland, Orkney and the Western Isles are much valued parts of Scotland and have been so for many centuries, including prior to the Treaty of Union in 1707. That would continue in the event of independence."
The submission goes on to say that the Scottish Government has been engaging in discussions with the three Islands Councils of Shetland to explore ways how, with the powers of independence, the needs of the islands could be recognised.
But Catriona Murray, joint ROTI press officer accused the government of being evasive, adding: "The implication is that they won't be able to hold referenda on the islands the week after the Scottish one, but they don't have the courage to say so explicitly," she said.