NB Liquor started charging five cents for the bags in June 2009 and donated the proceeds to the Nature Conservancy of Canada and Mothers Against Drunk Driving.
The corporation said bags will be free starting next Monday.
"Many retailers across Canada have discontinued the practice of charging for shopping bags and NB Liquor will eliminate the charge as a customer service enhancement," CEO Daniel Allain said in a statement Tuesday.
The Nature Conservancy of Canada said it always knew the program was a three-year initiative.
"Certainly as a not-for-profit organization, every little bit of funding helps," said Andrew Holland, a spokesman for the non-profit environmental organization.
"But we're thankful and we're grateful to NB Liquor for allowing us to participate in this initiative."
NB Liquor said the program has donated $40,510 to each organization since it was launched.
Susan MacAskill, a manager with MADD's Atlantic chapter, said she was confident NB Liquor would continue to collect donations and support the organization's programs as it has done in the past.
"We certainly appreciated the funds that have been contributed," she said.
"They have been a good corporate sponsor of MADD Canada and we will continue to work with them on various campaigns."
NB Liquor said eliminating the fee is in keeping with strategies to improve its business as outlined in a report commissioned by the Conservative government in 2010 and released earlier this year.
The review, led by Allain, recommended that NB Liquor establish more retail outlets, be shielded from political interference and remain in public hands.
The report also flagged potential losses, estimating that about $12 million to $15 million of annual revenue is lost by New Brunswickers purchasing alcohol in neighbouring Quebec. It called for a survey of customers close to Quebec to address that loss.
The corporation said Tuesday it has issued a request for proposals to open a seasonal agency store this summer in Shediac, a popular tourist spot about 25 kilometres northeast of Moncton.
NB Liquor said it also plans to launch more promotions and has made esthetic changes to the 48 corporate stores it owns and operates. The corporation has more than 70 agency stores in smaller communities that are owned and operated privately.
"We are dedicated to putting the customer first by showing them we have been listening to their concerns and addressing their needs," Allain said.