There is a hair-line difference in both the police checks. The main difference lies in the geographical regions where they are accepted.
National Police History checks are generally used by an organisation to determine suitability for employment, entitlement, licenses and industry accreditation purposes. It cannot be used for Immigration or visa application purposes.
AFP issued police checks are suitable for Commonwealth employment, visa applications, immigration, overseas adoption or overseas travel purposes. It is also an adequate police check for employment or entitlement purposes if you live or work in the Australian Capital Territory (ACT), Jervis Bay Territory or external Commonwealth territories.