The company said Mr Fowler was leaving because he did not want to continue commuting from Glasgow to Shanks' new headquarters in Aylesbury.
He has departed from the group after its dive in annual profits from pounds 27m to pounds 10m.
The fall, announced in June, followed a warning three weeks earlier and reflected a pounds 19m provision against losses from the construction division.
There were fears in the City that the move presaged another profit warning before the interim results, which are due in December.
Philip Morrish, an analyst at Smith New Court, said: 'The last two years have been very disappointing for Shanks fans and the next couple could prove to be equally difficult.'
Shanks' commercial manager, Michael Rundle, will look after the finance function until a new finance director is appointed, the company said.Reuse content