The video portrayed baby chicks being dropped on conveyor belts and thrown about by machinery, and sick or injured chicks being dumped into a grinder.
In his letter, Sechler called the organization a "radical" activist group, and accused it of planting a "mole" at the factory to "stage an attention-grabbing media show."
Tom Stone, director of sales and marketing for Bell & Evans, said the hatchery was audited yearly to ensure it complies with animal welfare standards.
A grinder, or macerator, is used by many companies to dispose of male chicks. Bell & Evans does not separate male and female chicks after they hatch, according to the company, and transports all healthy chicks to the farm. In recent years, the American Veterinary Medical Association has designated the macerator to be a humane form of death because death occurs "almost instantaneously."
Stone noted that the undercover investigator with Compassion Over Killing signed a form before joining the company acknowledging that it practiced a "zero tolerance" policy when it came to cruelty to animals.
Sechler's letter invited members of Compassion Over Killing to meet with Bell & Evans officials to discuss their concerns.
Erica Meier, head of Compassion Over Killing, said Thursday that the company had not contacted it directly, but that her group would reach out to the firm soon.
Bell & Evans has long portrayed itself as a pioneer in the organic foods movement and says it raises chickens on a vegetarian, antibiotic-free diet. Its products are sold to restaurants, butchers, and stores such as Whole Foods. The company is also known for ethics, declaring that "all of our chickens are humanely raised and compassionately handled."
In 2010, the company became one of two chicken producers in the country to render chickens unconscious with carbon dioxide gas before killing them.
In a 2009 post on the company website, Sechler fielded a question from a customer who asked if Bell & Evans discarded chicks by grinding them alive or smothering them.
"We at Bell & Evans like to think that we are very different from others in the poultry industry and do not practice the same standards that they do," Sechler said then. "You can be confident that Bell & Evans do not participate in those 'barbaric' methods."