Penalties for breaching licensing conditions include suspension or revocation of licence. Penalties for offences under the FTZ Act can include prosecution or imposition of a composition sum on the offence. In lieu of a suspension or revocation of licence, Singapore Customs may also carry out any of the following:

- Issue a letter of censure;

- Modify a condition of the licence;

- Direct the licensee to do, or to refrain from doing, such things as are specified in a direction to rectify the non-compliance or contravention; or

- Require the licensee to pay a financial penalty not exceeding $5,000 for non-compliance of a licence condition.

The penalty will be dependent on the severity and impact of non-compliance.