Israeli Chief of Staff Aviv Kochavi has threatened to storm the West Bank city of Jenin in case any of the two remaining prisoners arrived there.
These two in addition to four others had earlier snatched their freedom and fled from Gilboa prison.
Kochavi referred in an interview with Israeli Channel 12 on Wednesday to "the possibility of launching a large-scale military operation in Jenin" to arrest them.
"The interrogation with Zakaria Zubeidi shows that the prisoners planned to go to Jenin and it is possible that at least one of them has already arrived there receiving help and hiding there," Kochavi said.
"We will attack forcefully whenever there is a violation of sovereignty or harm to citizens,” he added.
"In Gaza, there is a need for two measures; humanitarian and economic assistance must be provided with one hand but this cannot be bypassed until the issue of captives and missing persons is resolved," Kochavi stated.
"The message to the organization that controls Hamas must be clear, strong and firm: We will use as much force as possible to prove to Hamas that there is no point in attacking us," he added.
Israel declared the state of alert two days ago ahead of Yom Kippur, the Jewish Day of Atonement, to avoid the scenario of another October War 1973, which started on this day according to the Hebrew calendar.
Moreover, the Civil Aviation Authority of Israel said the airspace would be closed for 29 hours.
In Jerusalem, thousands of police officers were deployed, with fears of potential suicidal attacks against Israelis. There will also be a heightened alert along the border with Gaza to deal with border riots and incendiary balloons.