Council leaders claim the decision announced by the Secretary of State Michael Forsyth last week will prevent the rationalisation of school provision which the Government wants local authorities to undertake.
Peter Peacock, convener of the council, added that a project for Lochaber under the private finance initiative, which the Government has tried to push for educational projects, will not now be possible.
Mr Peacock said: "It is appalling that at the very time we are discussing draconian cuts in education, the Scottish Secretary has removed our ability even to consider improving educational provision in Fort William. His decision defies logic. He should hang his head in shame. Never again should he lecture us on the need to act efficiently."
Val MacIver, convener of the education committee, said: "On the one hand the Scottish Secretary says that schools should not use the self-governing legislation as a means of avoiding rationalisation, and yet he gives the go-ahead to Fort William primary in the midst of a council review of provision in the area."
There are more than 600 surplus places around Fort William.
Mrs MacIver added that a recent visit to schools in the area had identified improvements in pre-school education and for children with special needs, and improvements in the fabric of primary schools and Lochaber High.
At Fort William primary, where more than 60 per cent of the 135 pupils attend following placing requests, improvements totalling more than Pounds 600, 000 had been identified, Mrs MacIver said. "Where is this money going to come from? Will it be taken out of the (council's) capital consents, resulting in other Highland schools having to wait considerably longer for their very much needed improvements?" Mr Forsyth said the parental ballot at Fort William, in which over 90 per cent of the two-thirds of parents voting had backed self-government, showed commitment to the future of the school. He said it was a "good, well-managed school with a substantial number of inward placing requests and an excellent local reputation".
The Rev Gordon Mair, chairman of the school board, described the decision as "common sense". He said the board "keenly anticipates co-operating with Highland education authority to further the education and equipping of our young folk for the future".
Mr Mair disputed the Pounds 600,000 cost of improvements, saying the figure was nearer Pounds 70,000. He thought the council wanted to close the school with a view to using the sale to finance repairs to other buildings.
Fort William primary may not be able to join the two other self-governing schools - Dornoch Academy and St Mary's Episcopal primary, Dunblane - before the general election. The Labour party has said that it will stop the opt-out if it takes office.
The press release announcing the Fort William decision contained other opting-out information. Mr Forsyth said he was minded to reject applications from Rockwell High in Dundee and two other Highland primaries, Lieurary in Caithness and Scotsburn in Ross-shire which, with 13 and 10 pupils respectively, are now likely to close.
Parents at the three schools have been given until January 24 to respond. The application by Rockwell had stopped the city council from merging it with Kirkton High. John Kemp, education convener, welcomed Mr Forsyth's decision, and said it should be "the beginning of the end of a long period of uncertainty for all those involved".