The clinic in the town of Trebic, 165 kilometers (100 miles) southeast of Prague concluded its investigation of what it earlier called a "regrettable case" by saying the mix-up was a result of "serious mistakes" made by two of its nurses.
They will be fired, one of them immediately, the hospital said in a statement Friday. It said the actions of five other staff members also contributed to the swap and they will be punished.
The mix-up came to light earlier this year when the father of one of the girls, Libor Broza, became suspicious because his daughter, Nikola - now 10 months old - did not resemble him. He had his DNA tested and learned he could not have fathered her.
Broza's partner, Jaroslava Trojanova, had a maternity test, and her results also were negative.
The other couple, Jan Cermak and his wife Jaroslava Cermakova, who were raising a girl they believed was their daughter Veronika, also had paternity and maternity tests done, and the results should be known next week.
The couples have already agreed to swap their daughters before the end of the year.
They reportedly plan to take legal action against the hospital. Broza and Trojanova plan to seek 10 million koruna (€365,000; US$510,000) in damages, reports said.
The clinic said it will hand over the results of the probe to the police, who have carried out a separate investigation of the case.
Hospital director Petr Mayer apologized to the parents and offered them help in solving the problem, the clinic said earlier.