South Korean President Yoon Suk Yeol speaks during a cabinet council meeting at the presidential office in Seoul, South Korea, Tuesday, Dec. 27, 2022. AP
The Monday intrusion by the drones -- one of which flew close to the capital Seoul -- prompted the South's military to deploy fighter jets and attack helicopters.
But despite a five-hour-long operation, the military failed to shoot down the North Korean drones, prompting widespread criticism over the response and an apology from the country's military.
President Yoon said Thursday that the incident was "intolerable" and added that the South should ensure that Pyongyang "realize that provocations are always met with harsh consequences".
"In order for us to achieve peace, we need to make overwhelmingly superior war preparations," he said during a visit to the state-run Agency for Defence Development.
"The overall response system against all flying objects invading our airspace, on top of drones, must be re-examined to quickly make up for deficiencies."
Yoon earlier this week slammed the military's handling of the incident and ordered the acceleration of a plan to launch a drone unit, which would include advanced stealth models, to carry out surveillance on Pyongyang's key military facilities.
The South's Joint Chiefs of Staff said on Thursday it would stage exercises focused on drones.
The incursion was the first time in five years that Pyongyang's drones had flown into the South's airspace and followed a recent flurry of sanctions-busting weapons tests by the North.
The North's leader, Kim Jong Un, said this year that he wanted North Korea to have the world's most powerful nuclear force, and declared his country an "irreversible" nuclear state.
Yoon said the North's nuclear weapons would not affect Seoul's responses to Pyongyang's future provocations.
"Regardless of whether the opponent has nuclear weapons or weapons of mass destruction, we should give a clear message to those who are provoking," Yoon said.