Cross River Commissioner Gyogon Augustine Grimah confirmed the bodies were recovered on Monday.
They went missing when the boat in which they were cruising capsized on Saturday.
Thirteen medical students across different universities in Nigeria were involved in the boat accident. Ten were rescued alive as soon as the boat capsized while the three went missing.
Two of the deceased students were from Ahmadu Bello University (ABU) Zaria and one from the University of Uyo, Akwa Ibom State.
The ABU medical students were identified as Mustapha Aminu Tukur and Kabiru Hamza.
The student from the University of Uyo was identified as Aisha Celestine Ogwu.