The prosecution also announced that two of the suspects have been detained an additional 15 days by a court order.
Villagers in Minya discovered the packages of the Chinese vaccine in a canal in the Abshaq villages near Beni Mazar town on Thursday.
The residents shared photos of the discarded doses on social media, causing an uproar in Egypt.
According to the prosecution, the investigations found that the discarded vaccines were allocated to the Minya Health Directorate and, after inspecting its inventory, it was found that there was a shortage of about 18,400 vaccine packages worth EGP 5,023,200.
The prosecution also added that it found a total of 13,412 packages in the canal that are now unusable, as they needed to be stored in a special cooling fridge.
This means that there are 8,944 packages that remain unaccounted for, the prosecution said in a statement.
Regarding the suspects, the prosecution stated that they are a pharmacist, a truck driver, and a warehouse keeper.
The pharmacist who works at the Minya Health Directorate was assigned to receive packages from Cairo to transfer them to the warehouse in the directorate using the driver.
Based on the investigations, the prosecution believes that there has been some form of negligence somewhere in the process. The defendants have so far presented two contradicting versions on how the packages were lost.
The Ministry of Health is currently operating nearly 17 vaccination centres in Minya, including Beni Mazar.
According to the latest official numbers, 14 million people in Egypt have been vaccinated against the coronavirus.
The government seeks to vaccinate 40 million people by the end of 2021.