Simultaneously, the boat was fired at from the Gaza Strip shore.
The Palestinians continued to swim toward the shore in the Rafah area. The navy soldiers shot and hit them.
IDF officials said that the two were carrying equipment tied to their body, which was suspected to be weapons.
Official Palestinian sources reported that one of the Palestinians was killed by the shooting and the other one was missing. Palestinian medical officials identified the slain man as Nazen Farhat, 27, from Rafah.
Ongoing smuggling attempts
Last Saturday, a navy ship sank a Palestinian fishing boat making its way from Egypt to the Gaza Strip in an alleged attempt to transfer weapons or to smuggle a wanted person from Egypt to Rafah.
The navy has recently been on high alert following estimations that the attempts to smuggle weapons or people via sea will increase. Large navy forces have been deployed in the area.
Egyptian naval forces are also operating in the area in cooperation with the IDF.
Before the IDF withdrawal from Gaza there were a number of attempts by Palestinian terrorists to swim to settlements in the area and carry out terror attacks. The attempts were thwarted by the navy.
Now, IDF officials said, the Palestinians are using the same methods in order to smuggle weapons.
AP contributed to the report