The death brings to 10 the number of Gazans killed in three separate tunnel collapses in two weeks.
The man was killed "as a result of a collapse of a mass of sand" inside a tunnel previously used to smuggle goods, a security source said.
He had been trying to restore the damage caused by Egypt flooding the tunnel, the source added.
A medical source identified him as Mussa Jaber al-Maadi, 24 and from Rafah in the southern Gaza Strip.
In late 2014, Egypt began setting up a buffer zone on its border with Gaza, and destroyed hundreds of tunnels it says are used for smuggling weapons and other items.
In September 2015, Egyptian forces carried out digging work that Palestinians say led to the flooding of the last remaining tunnels there.
On Saturday Israeli Energy Minister Yuval Steinitz said the tunnels were flooded by Egypt at Israel's request, before his office claimed the remarks were misinterpreted.
Hamas has accused Egypt of adding to the siege of Gaza by destroying tunnels which have long been used to transport people and goods in and out of the enclave of some 1.8 million inhabitants.
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