Gillis' parents, Jane and Robert Gillis, said they were happy to hear their daughter was safe but were concerned she was not released.
"We were so relieved to hear from our daughter after having heard nothing for 16 days," The Atlantic quoted Robert Gillis as saying after talking with his daughter for 15 minutes by telephone. "We still urgently appeal to the Libyan government to let her come home."
He said he considered the talk with his daughter a "hopeful first step" in her safe return.
Gillis, 34, was detained April 5 while reporting on the Libyan uprising for The Atlantic and USA Today.
She was taken outside rebel-controlled Brega, in eastern Libya, with two other journalists, U.S. reporter James Foley of the GlobalPost news agency and Spanish photographer Manuel Bravo of Germany's European Pressphoto Agency.
The three journalists were later moved to Surte and then to Tripoli, where they were kept in a coed military facility for about two weeks, Gillis said.
Gillis told her parents the three had communicated with each other from their cells by speaking through emptied-out electrical outlets.
She said she did not know what happened to Foley and Bravo after she was separated from them and transferred to the women's prison.