Doctors' groups have filed a petition at the Israeli Supreme Court seeking to halt air force jets from breaking the sound barrier over the Gaza Strip.
Israel continues to control Gaza's airspace, coastline and borders
The UN says the tactic is an abuse of human rights, causing widespread fear especially among children, and medics say it induces miscarriages.
The sonic booms from Israeli jets are designed to be a show of force to militant groups, correspondents say.
Israel evacuated its settlers and troops from Gaza earlier this year.
However, the Jewish state continues to control the territory's airspace, coastline and borders.
It has also continued to carry out air raids against what it says are militant targets.
The joint Israeli-Palestinian petition filed in the Supreme Court by the Gaza Community Mental Health Programme and Physicians for Human Rights-Israel says that according to international law, "the booms are collective punishment against the civilian population and thus illegal".
The head of the Gaza group, Dr Eyad Sarraj, a psychiatrist, has said that the sonic booms are having serious effects on children in Gaza, including anxiety, panic, fear, poor concentration and low academic success.
He also reports that the number of miscarriages among pregnant women increase during periods of frequent sonic booms.
The head of the UN Development Programme in the Gaza Strip, Khaled Abdul Shafi, said: "We at the United Nations have already submitted a letter of protest to the Israeli government urging them to stop... the sonic booming and the air raids immediately, because we simply think that this is a violation of basic human rights, especially rights of children to live in peace and to be educated in peace."
The Israeli military declined to comment.
"Because the subject is before the Supreme Court, the response will be given in that framework," the army spokesman's office said.