On Thursday, rescue services said seven men had been trapped in the collapse.
Five were rescued, but today the ministry said they had retrieved the body of Mohammed Abbas of Rafah, after announcing the death of a man named as Fadi Abu Dan.
A local civil defence official described the underground passage from the southern Gaza town of Rafah into neighbouring Egypt as a "trade tunnel".
The cave-in was caused by Egyptian flooding of the border zone in its campaign to stop smuggling, the official told AFP.
An Israeli blockade severely restricts the movement of people and goods into and out of the territory, and Egypt's sole border with Gaza has also remained largely closed since 2013.
The passages to Egypt are used for transit of commercial goods, cash, people and, allegedly, weapons.
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