The woman reported the deaths of her five-year-old son and two-year-old daughter to cantonal police on Thursday evening, the online edition of the Blick newspaper said.
“The exact cause of death is not clear,” police spokesman Werner Schaub told the paper.
Despite reanimation attempts, the children died at the scene.
The woman fled the house before the police arrived, but was found in the vicinity a short time later.
Police said the mother had self-inflicted injuries and it had not been possible to question her.
Neighbours told Blick the family had lived in a flat in the house since August.
The mayor of Flaach, Walter Staub, told the paper the family had financial problems and had received emergency assistance from the commune at the end of November.
“We are shaken by this news,” Staub said.
The case is reminiscent of the killing by a mother of her twins in Horgen, in the canton of Zurich, on Christmas Eve 2007, the paper said.