The body representing food and drink manufacturing in the UK warns there could be "barriers" to exporting English farmed foods if gene editing is allowed.
The government has launched a consultation on whether to green light the process, which it says could allow farmers to grow crops that perform better and reduce impact on the environment.
The process is highly restricted in the EU, after the European Court of Justice ruled in 2018 that gene editing must come under the same strict rules as genetic modification.
The Food and Drinks Federation (FDF) has welcomed the consultation - but told Sky News if gene editing is allowed in England, it could create hurdles for farmers exporting goods to the EU.
Helen Munday, chief scientific officer of the FDF, said: "We feel positive there are some benefits [to gene editing] but we must also understand what negatives there might be and those may be how we can trade our products.
"If Europe has a different view on this that may mean there are some barriers to trading products that are produced in this way."
She added: "We know that in other countries gene editing is considered not to be categorised as a genetic modification and clearly scientists feel that is not the right term for it because this is something that could happen in nature.
"But if there is that difference in definition then it needs to be understood; what the impact of that would be."
Gene editing can change the DNA of organisms in livestock and crops.
Environment Secretary George Eustice says the process could help farmers produce crops that are more resistant to pests, disease or extreme weather and to produce healthier, more nutritious food.
The process does not introduce DNA from other species, but rather speeds up the selective breeding process that farmers have carried out for hundreds of years.
Huw Jones, a professor in translational genomics for plant breeding at Aberystwyth University, told Sky News gene editing is different to genetic modification.
He said: "Gene editing is a tool. It uses so-called molecular scissors that can make targeted changes.
"Genetic modification is the movement of whole functioning genes from one organism into another.
"Whereas gene editing is making very targeted changes in the existing DNA of an organism. It's not adding any new DNA."
Critics say gene editing is a sticking plaster - and instead money should be focused on better farming techniques.