Dundee City Council will work with Apex Scotland, a charity that engages with young offenders, and will copy a model that is said to have helped reduce exclusions significantly at Dunfermline High in Fife, in the last five years.
The rate of exclusions in Dundee is two-and-a-half times the Scottish average, equivalent to 107 per 1,000 pupils, and far higher than other big cities, according to official figures.
The rate in Aberdeen is 62, in Glasgow 53 and Edinburgh 35. Dundee excluded 1,800 pupils in 2010/11 for transgressions including attacks on teachers, drug abuse and stalking.
The units will open from the start of the next school year, at a cost of about £70,000 a year each.
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