The wooden sarcophagi are ornately painted and covered in hieroglyphs, and were found stacked in two burial shafts, the ministry said in a statement.
They have not yet been opened, the ministry said.
Saqqara is a UNESCO world heritage site.
In March, Egypt reopened at the Saqqara site the Djoser's Step Pyramid, the first pyramid ever built, after a 14-year restoration costing nearly $8.8 million ($6.6 million US).
In July, Egypt restarted international flights and reopened major tourist attractions including the Great Pyramids of Giza after months of closure due to the coronavirus pandemic.
Yet despite reopenings and continued safety reassurances to international tourists, many concede that the key winter season starting in October is going to be tough, further straining the economy.
Other antiquities were unearthed in addition to the coffins.