The deceased were identified as Anjali and Shivani, both residents of Sangipur.
Pratapgarh SP Abhishek Singh said that both the girls had left their school during lunch time on Monday, informing their teachers that they had to head home for some urgent work.
After leaving the school, they called up their aunt and said that they were at Belhadevi temple. They asked her to arrange a pick-up for them.
Their family immediately contacted the concerned police station but the girls were not found at the Belhadevi temple.
According to the police, the girls had gone to a mobile shop in Lalganj area and asked the owner of the shop to call up their father so that he could pick them from here.
Suresh, the owner of the shop, called up girls' father and told him that both of his daughters were at his shop. In the meantime, the shop owner left the shop asking his mother to take care of the girls.
The girls did not stay there for long and left the shop before their father could reach there.
On Tuesday, the bodies of the girls were found floating in the river.
The SP said that the clothes of both the girls were intact which ruled out possibility of any sexual assault.
However, their hands were tied to each other with a piece of cloth.
The police suspect it a case of drowning and claimed that postmortem report would clear the picture.
The girls' family, however, suspects foul play in the matter.
( With inputs from IANS )