Danielle Tan
Chief Operating Officer
Preparing for a GMP audit in Malaysia? Discover the 10 most frequent audit failures in food, pharma & cosmetics — and learn how to fix them before they cost you certification.
In the food, pharmaceutical, and cosmetics industries, Good Manufacturing Practice (GMP) compliance is critical to ensuring product quality, safety, and regulatory conformity. However, even well-intentioned companies often fall short during GMP audits in Malaysia due to recurring nonconformities that can delay certification, result in penalties, or damage business reputation.
Whether you’re preparing for your first GMP audit or looking to strengthen your existing quality management system (QMS), understanding the most common GMP audit findings — and how to avoid them — is key to maintaining compliance and building buyer trust.
👉 Need help strengthening your GMP compliance?
Contact our team of GMP consultants today for expert guidance and practical solutions tailored to your industry.
What Are GMP Nonconformities?
A GMP nonconformity is any deviation from a GMP requirement, standard operating procedure (SOP), or regulatory expectation. These deviations are typically categorized into:
• Critical nonconformities – Issues that pose a direct risk to product safety or consumer health
• Major nonconformities – Serious failures in the quality system that could lead to unsafe products
• Minor nonconformities – Less severe deviations that may still impact GMP integrity
Top 10 Common GMP Audit Nonconformities
1. Incomplete or Poor Documentation
“If it’s not documented, it didn’t happen.” This GMP principle underscores the importance of accurate and complete records — a frequent GMP nonconformity in Malaysia.
Examples:
• Missing batch records
• Incomplete cleaning logs
• Unauthorized changes to SOPs
How to avoid it:
• Implement a controlled document management system
• Train staff on proper record-keeping practices
• Conduct regular internal audits of documentation
2. Lack of Personnel Training and Competency Records
Auditors often find that employees are performing critical tasks without proper GMP training or documented competency assessments.
How to avoid it:
• Maintain a training matrix for all roles
• Conduct annual GMP refresher courses
• Keep signed training records for each SOP and task
3. Improper Cleaning and Sanitation Practices
Inadequate cleaning procedures can lead to cross-contamination or microbiological risks, especially in food and pharmaceutical production areas.
Common issues:
• No cleaning validation
• Dirty equipment or surfaces
• Unlabelled cleaning chemicals
How to avoid it:
• Follow validated cleaning protocols
• Label cleaning agents clearly
• Document each cleaning activity in real time
4. Poor Pest Control Management
Pest infestations are a major red flag in GMP audits, particularly in food manufacturing plants.
How to avoid it:
• Engage a certified pest control provider
• Install fly screens, door seals, and traps
• Keep a log of inspections, treatments, and corrective actions
5. Improper Material Storage and Labelling
Incorrect storage conditions or missing labels can compromise material traceability and product integrity.
Issues may include:
• Raw materials stored at incorrect temperatures
• Expired materials not quarantined
• Missing “quarantine” or “approved” labels
How to avoid it:
• Use color-coded or barcoded labeling systems
• Store materials as per specified conditions
• Routinely review inventory for expiry dates
6. Failure to Calibrate Equipment
Instruments like thermometers, scales, and pressure gauges must be calibrated regularly to ensure measurement accuracy.
How to avoid it:
• Maintain a calibration schedule
• Use calibration stickers with valid dates
• Keep certificates from authorized calibration vendors
7. Inadequate Change Control Procedures
Uncontrolled changes to processes, equipment, or suppliers can lead to unintended risks and deviations.
How to avoid it:
• Implement a formal change control system
• Document all changes and their risk assessment
• Involve QA/management in approving changes
8. Lack of Environmental Monitoring
Especially in cleanrooms or sensitive manufacturing zones, failing to air quality, humidity, and cleanliness can lead to major non-conformities.
How to avoid it:
• Define environmental parameters in SOPs
• Install monitoring devices and maintain logs
Conduct periodic swab tests and surface inspections
9. Inadequate Handling of Deviations and CAPA
Some companies don’t document deviations or fail to follow up with a proper Corrective and Preventive Action (CAPA) process.
How to avoid it:
• Use deviation reports to track incidents
• Perform root cause analysis (e.g., using 5 Whys or Fishbone Diagram)
• Monitor CAPA implementation effectiveness
10. Outdated or Uncontrolled SOPs
Standard Operating Procedures (SOPs) must be current, approved, and easily accessible to all relevant staff in regulated industries.
How to avoid it:
• Use version control and approval signatures
• Retire outdated SOPs and maintain an SOP register
• Conduct periodic SOP reviews (at least annually)
How to Prepare for a GMP Audit in Malaysia
GMP compliance in Malaysia isn’t just about avoiding penalties — it’s about building buyer trust, market access, and operational safety.
To reduce the risk of non-conformities, consider the following best practices:
• Conduct Internal GMP Audits – Regular self-inspections help identify issues before external auditors do.
• Create a GMP Audit Checklist – Include all elements of your quality management system — documentation, training, equipment, facilities, and hygiene.
• Implement a Digital Quality Management System – Solutions like Scienta QMS help automate document control, training tracking, CAPA workflows, and audit readiness.
• Train Your Team – Ensure everyone understands GMP principles and their specific roles in maintaining compliance.
💡 Looking to streamline your audit prep?
Discover how a digital GMP system can transform your compliance process — from document control to audit trails.
Book a Strategy Call — Get a tailored roadmap to audit-ready compliance.
3 Must-Answer GMP Questions Before Your Next Audit in Malaysia
1. What documents are required for a GMP audit in Malaysia?
Batch records, cleaning logs, up-to-date SOPs, CAPA reports, and training records are the most commonly reviewed documents. Missing or outdated files are a frequent cause of audit findings.
👉 Audit coming up? Request a document check now!
2. Is a digital QMS system required for GMP compliance?
While not mandatory, digital quality management systems greatly enhance compliance. They reduce audit risks, ensure real-time traceability, and simplify documentation, training, and CAPA workflows.
👉 Still using manual systems? See how digital QMS simplifies audits.
3. What happens after a GMP audit — pass or fail?
After the audit, you’ll receive a report highlighting any nonconformities. If issues are found, you must submit a Corrective and Preventive Action (CAPA) plan. Certification is often granted once CAPAs are accepted and verified.
👉 Got audit findings? Let us help you fix the nonconformities.
Final Thoughts
GMP audits are essential checkpoints in maintaining product safety and regulatory compliance. By addressing these common GMP nonconformities, businesses can avoid costly setbacks and build a reputation for quality assurance and trust.
Proactive preparation, strong documentation practices, and a culture of continuous improvement are your best defenses against audit failures.
Strengthen Your GMP Compliance — Before It’s Too Late
🛑 Don’t wait for an audit to expose your weak spots.
Get expert help to fix nonconformities, optimise your system, and pass inspections — with confidence.
