The meeting was called in the wake of the deadly raid on a Gaza-bound vessel earlier in the week and the expected arrival of another ship, the Rachel Corrie, in the coming days.
However, the prime minister is still reportedly willing to show flexibility on Israel's blockade policy.
During Thursday's session, Netanyahu said: "We shall not allow the ships to reach Gaza. Not now and not later on. We intend to direct the Rachel Corrie ship to the Ashdod Port and transfer its civilian goods to Gaza following a security check."
Officials expect no confrontationEarlier, security officials estimated that activists aboard the Rachel Corrie will prefer to dock in Ashdod rather than to go on to Gaza. Officials believe the activists will seek to transfer their goods via land, while collaborating with Israel.
"If this is not the case, we will do everything to stop them without casualties," a security official said. "We are engaging in negotiations with whoever is out there."
Earlier Thursday, PM Netanyahu met with Quarter Envoy Tony Blair and told him he's willing to examine "creative ways" to bring aid into Gaza, after the goods are examined.
Blair told the PM he noticed that in the latter's speech Wednesday he made a distinction between Israel's legitimate right to prevent arms smuggling and the transfer of civilian goods, which should be allowed to come in.
The prime minister confirmed, stressing that every ship that may be smuggling missiles and rockets must be inspected.
Amnon Meranda contributed to the story