MPEDA has four Quality Control Laboratories in Kochi (Kerala), Bhimavaram, Nellore (Andhra Pradesh), and in Bhubaneswar (Odisha). All the four laboratories are accredited as per the ISO/IEC 17025 by the National Accreditation Board for Testing and Calibration Laboratories (NABL), a member of the International Laboratory Accreditation Co-operation (ILAC). The scope of accreditation covers testing of fish and fishery products for Chemical residues. The laboratories are also approved by the Export Inspection Council of India (EIC) for testing of fish and fishery products intended for export (commercial samples). The Laboratory at Head office has also got Food Safety Standards Authority of India (FSSAI) recognition for testing of fish and fishery products.

MPEDA has recently inaugurated another laboratory at Porbandar (Gujarat), which will be acquiring NABL accreditation and EIC approval soon.

The MPEDA QC Laboratories are equipped with high precision sophisticated equipments such as Liquid Chromatography Tandem Mass Spectrometers (UPLC-MS MS /HPLC-MSMS), Inductively Coupled Plasma – Mass Spectrometer (ICP-MS), High Performance Liquid Chromatographs (HPLC), Gas Chromatographs (GC-ECD), Gas Chromatograph- Mass Spectrometer (GC-MS & GC-MSMS), Automated ELISA Analyser etc, and all necessary supporting equipments/instruments.

The laboratories are undertaking implementation of National Residue Control Plan (NRCP) for aquaculture products as per EU requirement under directive 96/23/EC. Also undertakes testing of samples under Pre-Export Testing which is mandatory for export of seafood consignments.

MPEDA also have a microbiology laboratory in Kochi, set up with sophisticated instruments for testing, fish and fishery products, food and water. The Laboratory has two sections, one for conventional Microbiology testing and the other for molecular biology where advanced molecular biology tools have been set-up for testing of Viruses.