A method of monitoring and controlling temperature of a cargo in a refrigerated transportation cargo container comprising: measuring a temperature of a plurality of portions of the cargo disposed in the cargo container via a plurality of temperature sensors directed at the portions of the cargo; determining the cargo temperature, rather than the temperature of the airflow in the container by the temperature sensors, the temperature sensors being formed as non-contact sensors, namely thermal cameras or laser temperature sensors; computing an average cargo temperature from the measured cargo temperatures; comparing the average cargo temperature to an average cargo temperature threshold; changing operation of a refrigeration unit disposed at the cargo container in operable communication with the plurality of temperature sensors based on a result of the comparison; evaluating the measured cargo temperatures for localized cargo temperature variations; correcting the localized cargo temperature variations by changing operation of the refrigeration unit, wherein changing operation of the refrigeration unit comprises one or more of changing operation of a compressor, evaporator, evaporator fans, condenser fan or fresh air inlet of the refrigeration unit; transmitting the measured cargo temperatures to a controller in operable communication with the plurality of temperature sensors and with the refrigeration unit, the controller configured to change operation of the refrigeration unit; monitoring the cargo temperature for localized variations in cargo temperature by the refrigeration unit and by the cargo temperature sensors; monitoring cargo temperature data received from the plurality of cargo temperature sensors for individual cargo temperatures that vary from an average cargo temperature outside of a local cargo temperature threshold by the controller; and for example switching the evaporator fan to high speed operation to urge a stronger circulation of airflow throughout the container, thereby eliminating a hot spot or cold spot. measuring a temperature of a plurality of portions of the cargo disposed in the cargo container via a plurality of temperature sensors directed at the portions of the cargo; determining the cargo temperature, rather than the temperature of the airflow in the container by the temperature sensors, the temperature sensors being formed as non-contact sensors, namely thermal cameras or laser temperature sensors; computing an average cargo temperature from the measured cargo temperatures; comparing the average cargo temperature to an average cargo temperature threshold; changing operation of a refrigeration unit disposed at the cargo container in operable communication with the plurality of temperature sensors based on a result of the comparison; evaluating the measured cargo temperatures for localized cargo temperature variations; correcting the localized cargo temperature variations by changing operation of the refrigeration unit, wherein changing operation of the refrigeration unit comprises one or more of changing operation of a compressor, evaporator, evaporator fans, condenser fan or fresh air inlet of the refrigeration unit; transmitting the measured cargo temperatures to a controller in operable communication with the plurality of temperature sensors and with the refrigeration unit, the controller configured to change operation of the refrigeration unit; monitoring the cargo temperature for localized variations in cargo temperature by the refrigeration unit and by the cargo temperature sensors; monitoring cargo temperature data received from the plurality of cargo temperature sensors for individual cargo temperatures that vary from an average cargo temperature outside of a local cargo temperature threshold by the controller; and for example switching the evaporator fan to high speed operation to urge a stronger circulation of airflow throughout the container, thereby eliminating a hot spot or cold spot.