TG Daily claims that the actress no longer wished to be involved with the project following the announcement that Patty Jenkins would not be directing.
However, Portman entered a multi-picture deal with Marvel Studios when she signed up for the original Thor, and the company is said to have coerced her to honour the agreement.
The news follows reports that Captain America: The First Avenger actor Hugo Weaving has no desire to revisit his role as the Red Skull in future sequels, predicting Marvel will not force him to do so against his wishes.
Portman, Chris Hemsworth, Tom Hiddleston, Stellan Skarsgard, Idris Elba, Kat Dennings, Jaimie Alexander, Rene Russo and Anthony Hopkins will reprise their roles in Thor 2 alongside newcomers Christopher Eccleston and Adewale Akinnuoye-Agbaje.
The Alan Taylor-helmed Thor: The Dark World will be released on November 8, 2013.
Photo gallery - Chris Hemsworth on Thor 2 set: