Origin: Spirits of the Past - Any ideas on who makes the 'phone call'

Shunack did indeed make the call. Somehow he was able to detect that her Raban was active (possibly when she used it to open that door to escape the water). Notice that Shunack knows before Minka makes it aware to the soldiers of Toola's presence in the restaurant/bar.

After Toola talks to Agito's father she wanders off (on her way to the forest?) and is somehow encountered by Shunack. Seeing that he had more than one Raban, I can only guess that he made previous attempts to open E.S.T.O.C. with the Rabans found on the dead bodies in the cryogenic pods.