Excavation director Diego Barkan said 17 pits were found that had been used to store produce in the Early Bronze Age, from 3500 to 3000 BC.
"Among the hundreds of pottery sherds that characterise the local culture, a number of fragments of large ceramic basins were discovered that were made in an Egyptian tradition and were used to prepare beer," he said in a statement.
The excavation is the first to offer evidence of an "Egyptian occupation" in the centre of Tel Aviv 5,000 years ago.
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"This is also the northernmost evidence we have of an Egyptian presence in the early Bronze Age," he said.
According to the antiquities authority "beer was the Egyptian national drink and was a staple along with bread."
It said beer was consumed by the entire population of Egypt, regardless of age, gender or status.
"It was made from a mixture of barley and water that was partially baked and then left to ferment in the sun. Various fruit concentrates were added to this mixture in order to flavour the beer," the statement added.
Previous excavations carried out in Egypt's Delta region uncovered breweries that indicate beer was already being produced in the mid-fourth millennium BC, the Israeli authority said.