The mystery was resolved at 7 a.m. Sunday, when Israel announced that its air force had destroyed a tunnel running from the Gaza Strip south into Egypt and north into Israel under the delicate triple-border area of Rafah.
This is the third tunnel from Gaza that Israel has attacked in the past two months.
It has recently boasted of secret technology allowing it to locate and destroy them.
"(We) now hold a method, an organised system to destroy terror tunnels dug into Israel", he said. The tunnel could have also been used to transfer militants and arms for attacks in Israel or Egypt's Sinai Peninsula, he said.
The army said it was unaware of any injuries or deaths resulting from the incident.
"One of the Palestinian fishing boats came under direct fire from the Egyptian army late Friday near the Palestinian-Egyptian naval border, leaving a fisherman martyred", the Ministry said.
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He cautioned that "the tunnel underneath the Kerem Shalom border crossing was an operation of deception not only against the Egyptians, but against Israel too".
Israeli military spokesman Lt. Col. Jonathan Conricus told CNN the strike was carried out Saturday with "necessary coordination" with Egypt. There were no reports of injuries in the destruction of the tunnel.
"The Hamas terrorist organization is responsible for everything happening in and out of the Gaza Strip", the press release added.
Israeli Prime Minister Benjamin Netanyahu said the tunnel was a "main Hamas infrastructure".
Israel had been monitoring the tunnel for an "extended" period, but Conricus would not specify how long.
The tunnel's design was out of the ordinary, not matching the size of some larger tunnels and lacking the domed roof of smaller attack tunnels. It reached underneath the Kerem Shalom border crossing and below diesel and gas pipelines into Gaza, penetrating some 180 meters inside Israeli territory.