The method is blamed for the death of at least one Palestinian detainee last year and has been widely criticised as torture.
The ruling came during a petition by a Palestinian militant who is suspected of organising a suicide-bombing attack that killed 21 Israelis a year ago.
The court accepted the State's argument that the suspect, Abdul Halim Balbisi, may have been withholding information on another planned attack on Israelis in the near future.
In effect, the court removed an injunction granted on 24 December against using "physical force" in the interrogation of Balbisi. He sought court intervention following his arrest at an unknown date. In his petition, he complained he was being violently shaken.
Despite the injunction, interrogators extracted a confession from Balbisi that he organised the suicide attack made on 22 January last year.
He told interrogators he had prepared three bombs at his home but only two suicide bombers showed up. He said he left a third bomb in its hiding place for a future attack, according to court documents obtained by Associated Press. Balbisi later directed Israeli agents to the unused third bomb.
The court added that its ruling did not amount to a permit for allowing illegal interrogation methods in the future.
The Shin Bet has been allowed to use the method by a ministerial committee on a limited basis. The violent shaking method cannot be used without authorisation from the Shin Bet chief.
The method usually involves grabbing a detainee by the collar and vigorously shaking his body back and forth for three to five minutes, according to the Israeli human rights group B'tselem.
Combined with sleep deprivation, it can cause brain clots and brain damage.Reuse content