SAHPRA Engagement Portal – Type II Pilot Variation Applications: Submission Window and Fee Processing Clarification
- Sharan Murugan
- 1 hour ago
- 3 min read
In January 2026, the South African Health Products Regulatory Authority (SAHPRA) issued an important communication to stakeholders regarding Type II variation applications submitted under the Type II Pilot Programme. The update provides clarification on submission window compliance and temporary fee processing arrangements due to a system-related pricing limitation in the SAHPRA Engagement Portal.
Background and Context
SAHPRA acknowledged that certain applicants experienced challenges in finalising payment for Type II variation applications due to differences in pricing calculation methods within the Engagement Portal. The authority confirmed that the interpretation of the calculation module has now been aligned with industry’s understanding and that system development changes have been requested.
However, the January Type II Pilot submission window was scheduled to close before the updated pricing changes could be implemented. This raised concerns that applicants with completed submissions might not be able to finalise payment within the window. Following internal review and executive alignment, SAHPRA confirmed an interim process to manage affected applications.
Submission Window Compliance
SAHPRA clarified that Type II variation applications will be regarded as compliant within the January submission window if:
The application was created in the SAHPRA Engagement Portal on or before 30 January 2026; and
The complete eCTD submission sequence was uploaded to the designated FTP location on or before 30 January 2026.
Applicants were specifically advised not to make changes to the eCTD upload after 30 January 2026. Any modification to the FTP-uploaded sequence after this date would result in the submission being considered non-compliant. The portal-generated submission creation date and FTP upload timestamp serve as the definitive record of submission timing.
This clarification ensures that technically ready applications are not disadvantaged due to temporary system pricing constraints.
Fee Processing and Financial Completion
SAHPRA identified that, for certain Type II variation combinations, the portal was unable to correctly calculate the applicable gazetted fee due to a system pricing limitation.
To address this issue, SAHPRA introduced a temporary process:
Applicants are not required to make payment against an incorrect sales order.
Applicants should complete the submission process up to the stage of creating a Sales Order (without payment and without uploading proof of payment) and upload the eCTD sequence to the FTP site in the meantime.
Once the calculation methodology is corrected in the system, a recalculated Sales Order will be generated.
Applicants may then proceed with payment against the recalculated order and upload proof of payment.
Application Support will review the updated payment and allow confirmation of the FTP upload.
This interim mechanism ensures regulatory continuity while technical updates to the portal are completed.
Processing Controls and Regulatory Safeguards
SAHPRA further clarified that no technical assessment outcomes, regulatory recommendations, or approval decisions can be initiated or finalised until the recalculated fee has been paid and proof of payment uploaded.
The authority emphasised that:
The temporary arrangement applies only to Type II variation applications submitted under the Type II Pilot Programme that meet the defined criteria.
The measure is implemented solely due to the confirmed system limitation for the January submission window.
The arrangement does not establish a precedent for future submissions.
These controls maintain regulatory integrity while providing flexibility to applicants during the system adjustment period.
By defining clear submission window criteria and implementing a temporary fee-processing pathway, SAHPRA ensured that applicants are not penalised for system-related constraints while maintaining strict oversight of payment validation and assessment initiation.
Applicants submitting Type II variation applications under the Pilot Programme should follow the clarified process carefully and monitor further communications once the portal fee calculation module has been fully updated.
Reference
For more details on this official communication, please click the above link to access the full guidance document.