The 34-year-old, who had a long competition break, ran the time 1.36 in Lisbon in March.
However, she had not made herself available for doping control six months prior to the competition, which is a requirement. This means that the result, the Swedish record, is invalidated by Anti-Doping Sweden, according to the association.
Aregawi has been denied her application for exemption from the six-month rule.
Abeba Aregawi, born in Ethiopia, began competing for Sweden in 2012 and was then a world star. She then took, among other things, VM gold for Sweden on 1,500 meters in Moscow 2013.
Aregawi tested positive for doping in 2016 but was acquitted the same year since her levels of the substance meldonium were below the anti-doping agency WADA's limit values.