50-year-old Parwan Singh committed the twin murders yesterday when the mother of the two sisters had gone out for work, SSP Nivedita Kukreti said.
He has been arrested and sent to 14 days' judicial remand by the CJM's court.
He confessed to killing the sisters - one aged 13 and the other 3 - in their room located behind the gurudwara but the motive behind the crime is not clear, she said.
The story narrated by the accused is not convincing and the post mortem report is still awaited, Kukreti said.
However, the mother of the two girls told police that the Sevadar's intentions did not appear to be right and the girls were afraid of him, she said, adding that the matter is being investigated from all possible angles.