Rahma, 18, and Jibril, 13, (not their real names) are traumatised and shocked even as they stay at a temporary rescue centre in Tana River County.
The man they have known as their father had defiled one of them for years and the other for months.
According to a guardian who came to their rescue, the man had defiled the elder daughter for more than four years before he turned to the younger one, whom he first attacked in March.
"These children have been through a lot, and their mother could do nothing about it since the father is a hostile person, hence she feared he could even kill them," said the guardian, who did not want to be named.
She said the girls’ mother could not bear it anymore when the man turned on his younger daughter and shared her pain and frustrations with close confidants, who in turn informed elders.
But when the man got wind that his evil secrets had leaked, he started threatening the children and frustrating efforts to obtain justice for them.
"I feared it would get worse, so I reported the matter to the Bura gender officer, who in turn took the matter to the police," the guardian said.
The cases were reported to the Bura Police Station under OB 28/7/2022 and OB 29/7/2022, but the suspect has allegedly been intimidating the children and officers involved in seeking justice for the girls.
To save the children from distress, a team of human rights groups led by Groots Kenya whisked the girls to safety.
"We have them in a safe place for guidance and counselling, since they are traumatised and would not wish to continue staying in an environment that is disturbing to them psychologically," said Rahma Adan, Groots Kenya coordinator.
Hawaa Abdigafoor, Tana River County gender-based violence and adolescent focal person, said a hospital had taken samples from the girls for testing.
"Our preliminary results show they have been defiled. We shall give more information upon conclusive feedback of the samples," she said.
Meanwhile, the police were tracking down the suspect, who had gone into hiding.
Bura police boss Ali Ndiema said a team was sent out to find him as he could not be reached on his official phone number.