The survey included interviews with 2000 employers across Scotland and found that 17% of employers had gaps to fill.
The survey showed that two-thirds of employers who reported a skills shortfall referred to higher operating costs, problems meeting customers' expectations and challenges arising from new working practices or technology.
About half of the survey's respondents had not funded or arranged training for their staff.
Dr MacDonald said the findings would help to ensure that plans to address skills shortages are targeted effectively. He said: "This is particularly relevant for the construction sector, and we have made significant resources available to address skills needs."
CITBConstructionSkills chairman Sir Michael Latham said that skills shortages in Scotland are less severe than other parts of the UK.