Ruth Abakah, Priscilla Blessing Bentum, Ruth Love Quayeson and Priscilla Mantseabea Koranchie had been kidnapped on July 29, August 17, December 4 and December 21 respectively.
The remains of the girls were found in a septic tank at Kasaworodo, a suburb in Takoradi.
Police believe they are victims of a kidnapping and murder syndicate in the Takoradi area.
The main suspect, a 28-year old Nigerian, Samuel Udoetuk Wills, was arrested in the Western Region, while his accomplice John Orji, was arrested at the Aflao border in the Volta Region.
A third suspect, known only as Chika, have been arrested in Nigeria.
The news of the death of the four girls sparked an uproar as many citizens demanded the resignation of the Director of the Criminal Investigation Department (CID) Maama Tiwaa Addo Danquah who handled the case.