Three-quarters of the 700 companies employing between 30 and 2,000 staff,
surveyed by consultants Ernst & Young, said on Thursday it was "rather" or "very" difficult to find enough qualified workers.
The survey which showed the worst-hit sectors were construction and energy, followed by trade, services and industry.
The majority of the small and medium-sized enterprises (SMEs) questioned said the difficulty in finding staff hit their turnover, with 64 percent complaining turnover was reduced by three percent higher.
Based on the survey results as well as official statistics on German companies, Ernst & Young calculated the businesses were missing out on around €33 billion ($44 billion) of revenues.
Peter Englisch, head of the SME division at Ernst & Young, said that although the problem had long been felt across Germany, small and medium-sized companies were particularly affected.
He said they were suffering due to not being as well-known as larger companies and being based away from the larger cities which workers are attracted to.
To counter the problem, the companies surveyed said they relied upon continuous staff training and paid particular attention to older workers – a key factor given Germany's ageing population.
More companies are also trying to recruit from abroad after the government extended the list of professions for which a work permit can more easily be obtained. They now include electricians, nurses and care staff.