Stockholm police spokesman Ola Österling said the prosecutor leading the investigation into the two women had ordered their arrest.
“We executed that decision when the plane arrived in Stockholm in the afternoon,” Österling told AFP. A third woman had been taken in for questioning, he added.
A statement from the Prosecution Authority Monday said multiple investigations were under way against men and women returning from areas that had been controlled by the Islamic State group (Isis or IS).
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“The international crimes that are relevant for people for people returning from Isis-controlled areas are war crimes, genocide and crimes against humanity,” public prosecutor Reena Devgun said in the statement.
“Sweden has an international committment to investigate and prosecute these crimes,” she added.
The Prosecution Authority added that it could not comment on individual cases or the number of investigations under way.
But public broadcaster SVT reported that at least one of the women arrested was being investigated for war crimes, genocide and crimes against humanity.
SVT also reported that the women who had returned Monday had been staying in camps in northern Syria but had been deported by Kurdish authorities after deciding they did not have enough evidence to prosecute them.