Several departments of the Food & Environment Health Agency (Fera) have merged with the Animal Health and Veterinary Laboratories Agency (AHVLA).
The new organisation will be known as the Animal and Plant Health Agency (APHA) and was created to better respond to, and contain, disease across both the animals and plants sectors.
The four Fera departments that are being merged into APHA are the Bee Inspectorate, the Plants Health and Seeds Inspectorate, the Plant Variety and Seeds Group and the GM Inspectorate.
Other Fera departments will continue to function as an independent agency for the time being, Defra said.
APHA will start work from 1 October, with current chief executive of AHVLA, Chris Hadkiss, taking on the same role at the new agency.
A statement said that animal and plant health inspectors have a strong history of working together in times of disease emergency, and this will be made easier when they are part of the same organisation.
It added that APHA will also play a vital role in stopping invasive non-native species entering the UK.
Environment minister Lord de Mauley said the move will enable joined-up working on plant and animal diseases and pests, and will increase the UK’s resilience and flexibility to respond to emergencies.
AHVLA chief executive Chris Hadkiss said: “I am really looking forward to building on the excellent reputation of both the Fera Inspectorates and AHVLA. Together as one agency we will be working for a healthier environment and economy.”