The EPR scheme aims to increase recycling rates by passing on the costs of recycling from local authorities to the companies selling the products.
However, because the fee is calculated by weight, heavier materials like glass will be taxed more than lighter alternatives such as single-use plastics.
Critics argue that this approach unfairly penalise glass, despite its environmental benefits – such as that it is endlessly recyclable and chemically inert.
Sean Murphy, Managing Director at Encirc, said: “The new glass bottle tax is an economic and environmental own goal, hitting UK firms producing packaging that is far better for the environment than plastic.
“This tax will hit everyone - in the supermarkets, pubs, and glass factories that create thousands of jobs.
“It is a bitter blow for businesses such as ours which are investing heavily in green technology.”
The tax is due to affect glass wine and spirit bottles the most.
Under the new government policy, a standard bottle of wine will cost an additional 9p, while the cost of a 330ml beer bottle will rise by around 4p.
Spirit bottles will cost an extra 11p under the levy.
These price increases could be passed onto consumers.
For example, John Lewis reported that EPR could cost the business £29 million.
Mr Murphy added: “The government must hit the pause button on this.
“An arbitrary measurement based on the weight of materials unfairly penalises glass and just doesn’t work.”