Likely to be based in Edinburgh, it will be run by a small group of four to six people, headed by a chief executive who will be paid around pound;80,000 a year. Their aim will be to bring to Scotland the world's best practice and practitioners, and adapt the expertise to the country's needs.
Peter Peacock, Education Minister, commented: "The importance of the quality of school leadership cannot be underestimated. Excellence in leadership makes all the difference to a child's success at school and in later life.
"Today's announcement is another exciting partnership with the Hunter Foundation and will underpin our drive for ambitious, excellent schools. It will help schools and education authorities access the best possible leadership development opportunities."
Tom Hunter, the foundation's chairman, said: "This is about again raising our overall game in education to ensure that Scotland leads the world in delivering the very best in leadership.
"This will not be a delivery vehicle, more a small, highly effective team of professionals that can determine gaps in the marketplace and define solutions to those gaps. In addition, it will provide a dynamic source of knowledge to the market in the pursuit of excellence for all."
The Executive and the foundation envisage they will provide funding for up to five years, with the foundation contributing pound;100,000 a year to estimated overall costs of pound;500,000 per annum.
Ewan Hunter, the foundation's chief executive, told a conference on education reform in Edinburgh this week that there were major gaps in the present system. "There are some clearly odd disconnects in the process and delivery of excellent teachers and leaders in Scotland's schools and local authorities."
Mr Hunter cited the lack of development opportunities for those who train teachers and the need to do more to fast track the classroom and local authority leaders of tomorrow.
He also criticised the existing Scottish Qualification for Headship. "Who was responsible for designing that? It's barking," he said. It was "too process-driven" and did not enthuse would-be heads to lead an organisation.
The Executive and the foundation also announced this week that they are to fund three pilot programmes, worth pound;500,000, aimed at expanding leadership beyond the top ranks. It will be part of the Columba 1400 initiative and will include leadership development for children as well as teachers, promote leadership development involving a whole community and trial "collegiate working" with several schools and authorities.
The fruits of all these endeavours are intended to feed into the Executive's first tranche of 20 "schools of ambition" (page four).
Ewan Hunter said: "We are funding the initiative for leadership development and the new Columba 1400 pilots on our usual basis - pilot, prove, adapt.
We are not here as a substitute for the taxpayer; we are here as a funder of risk innovation that, once proven, becomes policy."
He added: "If this venture is successful, for example, it will not need to exist in a few years' time."
In his speech to the conference, Mr Hunter pledged to work with the education world. "Change imposed from outwith is the most fragile of changes, so fragile in fact that you would never attempt to apply it," he said.
"Change from within is the single most powerful methodology for effective change you will ever see; our new leadership programme will assist in effecting internal change so that we can all be determined to succeed."
The foundation's latest involvement follows its investment in the Executive's Determined to Succeed enterprise education programme, the Columba 1400 headteacher leadership academy and the new approaches to teacher education being led by Aberdeen University.