Galina Ryabkova took her boys, aged four and seven, from their apartment on the eight floor of the housing block in the Moscow region town of Dolgoprudny to a balcony of the 15th floor of the building, investigators said.
"Then the mother threw the two children from the balcony. They died of their injuries received in the fall," the Investigative Committee said in a statement.
It said that the woman had been detained after the incident on Sunday afternoon and she would be subjected to a psychiatric examination.
During interrogation "Ryabkova said that she was sick of the children and she had decided to get rid of them," it said. The children were not going to kindergarten but were being educated at home.
The woman, originally from the southern city of Volgograd, was planning to divorce her husband and had attempted suicide even before marriage, the statement said.
The deaths of the children have shocked Russia and also raised questions over whether the social services are doing enough to protect children from potentially dangerous parents.
"I saw one of the boys, he was lying on his back in green shorts and he had something green in his hands, some kind of toy," eyewitness Lidia Kochergina told state Channel One television.
Channel One said that the mother had tempted her children up to the 15th floor by promising them that they would throw paper planes from there.
The lifenews.ru tabloid website said that her husband, named as Sergei, was in a state of shock and had barricaded himself inside his home and was unable to answer any questions.