The school in Skerries, which has three pupils, will close on July 4 and pupils will continue their education in Lerwick, staying in hostel accommodation.
The announcement yesterday brings to an end a decades-long battle over the future of the schoool. Shetland Islands Council has been trying since the mid-1990s to close the small island school.
However, last December councillors decided by the narrowest of margins - the casting vote of council convener Malcolm Bell - to close the secondary department, saving an estimated £73,000 per year.
The community had hoped Mr Russell would at least call in the decision.
But a Scottish Government spokesman said: "After careful consideration of Shetland Islands Council's proposal to close Skerries Secondary Department and the representations received, ministers have concluded the council has fulfilled its obligations under the 2010 Act and consequently will not be issuing a call-in notice for this proposal."