Lieberman held consultations with senior IDF and Shin Bet officials as well as with the coordinator of government activities in the territories (COGAT) and instructed them to be prepared for "additional steps if the violent incidents continue."
Other measures could include more restrictions at Kerem Shalom, Gaza's prime commercial crossing point and the only one with Israel.
Lieberman cited Friday's riots at the fence dividing Gaza and Israel as contributing to his decision, in addition to the midweek beach protests in which fishing boats and protesters gather at the northwest end of the Gaza Strip where its sea and land barriers meet with Israel.
Some 20,000 protesters gathered Friday along the Gaza border fence to take part in the weekly border clashes, burning tires and hurling explosive devices at IDF troops and covering the adjacent Kibbutz Kerem Shalom with thick smoke.
The IDF said that some protesters crossed the fence to throw grenades on Israeli territory before returning to the strip.
The IDF responded with crowd dispersal measures, which for the first time included the use of sponge-tipped bullets.
Three Palestinians aged 12, 24, and 28 were killed during the skirmishes.
No Israeli casualties were reported.
In response to "grenades and explosive devices" hurled at troops during the protests, an Israeli Air Force (IAF) aircraft carried out two airstrikes on Hamas military positions in the Gaza Strip.
Ahead of the Friday clashes, the IDF closed to traffic at least four roads in the vicinity of the Gaza Strip border due to fears of a possible escalation of hostilities in the area.
Throughout the day Friday, at least seven fires broke out in the Gaza border communities as a result of incendiary balloons being launched into Israel from the strip. Firefighter teams gained control over the fires.
Prime Minister Benjamin Netanyahu addressed the situation on the southern border during Friday's meeting with German Federal Minister for Foreign Affairs Heiko Maas. "Israel would take strong action against Gaza for every action against Israel and the residents of the south," he stressed.
The military brass headed by Chief of Staff Lt. Gen. Gadi Eisenkot toured Friday the Gaza border area, after which they held a situation assessment.
During the riots, the newly elected leader of the Palestinian Islamic Jihad, Ziad al-Nakhala, spoke publicly for the first time since his official appointment a week ago, warning the Gaza border communities’ residents.
“Death is life for our people and life for our children, and capitulation is our death. The Israeli aggression against the 'March of Return' campaign and the killing of our people must stop,” he stated.
“The resistance must take responsibility for this. It has the ability to turn the Gaza border region and its settlements into a place that is not life worthy," Nakhala threatened.
"We say to (Palestinian President) Mahmoud Abbas: our people's historical enemy doesn’t understand words of peace and compromise, but of war and sanctions," Nakhala said addressing Abbas, adding "We've recently worked to strengthen our relations with all parties, especially with Hamas."
The Associated Press contributed to this story.