The agreement sets out a code of practice that retailers and their suppliers, including growers, should follow if they suspect that labourers are being abused.
For example, it details how the GLA will work with the industry to make sure proper standards are in place and how "intelligence" should be reported to the authority.
The main supermarkets - Asda, Co-operative Food, Iceland, Marks & Spencer, Morrisons, Sainsbury's, Tesco and Waitrose - have signed up to the protocol, which has been reached after two years of extensive negotiations with the retailers, the NFU and the Fresh Produce Consortium (FPC).
GLA chairman Paul Whitehouse said: "Much has been achieved in recent years in protecting workers from abuse in the UK food industry, but problems still exist.
"The Equality and Human Rights Commission's report into the meat industry highlights some of the challenges that remain. This protocol shows that everybody in the industry is determined to make sure that workers are treated fairly and legitimate businesses are not undercut by rogues."
FPC chief executive Nigel Jenney commented: "The consortium welcomes the introduction of this protocol, which recognises the importance of equal partnership between retailers and their suppliers to maximise the protection of vulnerable workers.
"The GLA has made great strides by working with the supply chain to bring rogue gangmasters to book and eliminate labour abuse across the fresh produce industry."
NFU chief horticultural adviser Philip Hudson said: "The NFU is delighted to be able to support this protocol, which recognises the importance of the GLA working with retailers and suppliers in the shared mission of preventing the abuse of workers."
Ethical Trading Initiative director Dan Rees added: "This protocol represents a great opportunity to make a real difference. Supermarkets and suppliers can help drive improvement in conditions for the most vulnerable workers in the UK food industry."
The launch of the protocol, which will be reviewed annually, follows two consultations held in 2009. The GLA went back to the drawing board after the NFU and the FPC feared that some of the proposals in the original protocol could have left growers out of the loop and insisted that it should explicitly state that suppliers and labour users were included in all negotiations and briefings.
For example, the GLA originally stated how it would like to meet up regularly with retailers so that inspection findings could be disseminated to inform best practice.
But the NFU feared that this protocol ran the risk of alienating growers by treating them as part of the problem rather than the solution to stamping out the exploitation of workers.
NFU horticulture board chairman Sarah Pettitt, who worked with the GLA on the new rules, said: "The launch of the GLA protocol is the culmination of two years of discussions between the NFU, the FPC and the GLA."
She added: "I am pleased that during this consultation the GLA took on board many of the concerns expressed by the NFU on the detail of the operation of the protocol. It now provides a common platform for the industry and the GLA to work together to prevent the abuse of workers."