The workers died after inhaling toxic gas inside the tunnel, the agency said in a statement on Saturday.
The bodies were recovered on Saturday and were sent to a hospital in the town of Rafah.
A Palestinian security source said on Friday that four workers had gone missing and that ten others suffered after inhaling toxic gas while repairing a tunnel destroyed by the Egyptian army.
There was no comment from the Egyptian side on the claim.
Reeling from a decade-long blockade by Israel, the roughly 2 million inhabitants of the Gaza Strip have come to rely on the cross-border tunnel network for the import of badly-needed commodities, including food, fuel and medicine.
Since Egypt's 2013 military coup against President Mohamed Morsi, a Muslim Brotherhood leader, the Egyptian authorities have cracked down on the network of border tunnels.
In recent months, the Egyptian army has been methodically flooding the network of cross-border tunnels linking Gaza to Egypt's Sinai Peninsula.
In 2014, Egypt began building a "buffer zone" along its border with Gaza following a spate of militant attacks on Egyptian security forces.