Root Cause Analysis and CAPA - Why FDA Keeps Calling Them Out

If you skim FDA Warning Letters week-to-week, one theme pops out: firms routinely struggle to identify true root causes and to build CAPAs that work. Two recent Warning Letters (Apotex Inc. and Scientific Protein Laboratories, LLC) show the same recurring patterns from different operations.

What FDA criticises

1) "Testing into compliance" and shallow investigations

At Apotex, the FDA describes repeated leak-test failures on critical aseptic equipment between Sept 2023 and Apr 2025. Production personnel "repeatedly performed leak testing until they obtained passing results instead of investigating the root cause". Furthermore, the FDA judged the firm's post-inspection CAPAs reactive and inadequate because they didn't demonstrate systemic fixes or timely impact assessment on distributed batches.

2) Failure to expand scope and act with urgency

Still at Apotex, an incompatibility between a solution product and the cap liner led to corrosion and leakage. The risk was rated "Undesirable / High," yet no market action occurred at the time. Later, recalls followed the inspection. FDA faulted the firm for not broadening the investigation to all potentially affected batches and for delayed actions.

3) Weak preventive controls and CAPA effectiveness

Apotex also drew criticism for aseptic controls: deteriorated or contaminated equipment surfaces, taped "false covers," glove breaches (including a 6-mm hole closed with a cable tie during processing), and deficient environmental monitoring (e.g., lack of continuous non-viable particle monitoring in critical areas). The FDA asked for an independent assessment of investigation and CAPA systems, highlighting the need for stronger maintenance and oversight.

4) Investigation and CAPA not convincing

According to the FDA, Scientific Protein Laboratories (SPL) failed to establish and follow procedures for investigating critical deviations/OOS. Even after the firm revised procedures to require root cause analysis, CAPAs for critical/major investigations, and client holds, the FDA still found the response inadequate. Root causes weren't adequately identified, investigations weren't expanded, and CAPA details and supporting evidence were missing. The FDA is now demanding a comprehensive, independent assessment of investigations and CAPA effectiveness.

What these Warning Letters are saying about RCA and CAPA

Don't chase a pass, chase the cause: Re-testing until you pass without understanding the failure ("testing into compliance") is itself a signal of weak culture and method. Procedures should require stopping if necessary and investigating after failures and don't allow serial re-tests to mask sporadic or intermittent faults.

Broaden the lens: Good investigations expand scope: adjacent lots, similar products, shared equipment, common materials, and historical trends. FDA repeatedly asks for retrospective reviews and effectiveness checks also in other Warning Letters published in the past months.

Tie risk to action speed: If risk is "High/Undesirable," actions must be urgent and visible (market action, quarantines, client holds). Delays, even if ultimately corrected, undermine confidence in the quality system.

Quality Oversight is part of CAPA: Both letters emphasise quality and operations management accountability, ensuring timely detection, repairs, upgrades, and trend reviews.