The British Beer & Pub Association (BBPA) has welcomed some of the planned changes to the apprenticeship levy, announced by the government earlier this week.
But the association said it was also concerned employers would not be able to use contributions for existing apprentices.
From April 2017, a levy will be introduced on company payrolls, which ministers say will help to double government spending on apprentices.
Under the scheme, businesses will be able to use vouchers from the levy to pay for apprenticeships.
Latest changes to the levy include an extra 20% of funding to train 16 to 18-year-olds and 24 months for businesses to spend the vouchers, up from 18 months.
The government also said there would be more money for employers to train apprentices in the poorest parts of England and for employers who take on apprentices under 24 who are in care or have special educational needs.
Brigid Simmonds (pictured), chief executive of BBPA, said: "Increasing the time during which employers can use the funding from their levy contribution from 18 months to two years is welcome, as is the increase in the level of funding available to employers using the food and drink engineer standard.
"We remain concerned, however, that employers will not be able to use their contributions for existing apprentices already working in their business. This seems to penalise employers in our sector that have bought into the scheme, and already invest heavily in apprentices.
She added: "Setting up a new working group to look at how funds can be used within the supply chain is very welcome. The BBPA will continue our contribution towards this debate, as it has a huge effect on leased and tenanted pubs and suppliers to the brewing industry, but it is unfortunate that no change looks likely before 2018."