The firm called for an urgent review of the system, which has come under attack from business groups since it was launched last year.
Around 400 more placements could be created if changes were made such as allowing the business to use the levy to cover costs such as travel and accommodation on training courses, said the Co-op.
Helen Webb of the Co-op said: “The Co-op is recognised as an apprenticeship front-runner, having employed more than 4,000 apprentices since 2011.
“We share the Government’s vision, but there needs to be an urgent review of how the levy works in practice.
“We support the principle that 20% of an apprentice’s time is spent off the job in training, but funding guidelines mean that we can’t use our levy.
“This costs us more than £5 million a year to finance our apprentices when they are out of the business, reimbursing their travel costs or paying for someone to cover their duties.
“Our business is currently having to spend an additional £3.2 million to support these costs as it can’t be claimed through the levy. If we could use the levy to cover these costs we could offer up to 400 more apprenticeship roles.”