He was protesting at what the Israelis saw as a breach of faith when Mr Cook crossed a border checkpoint near the contentious Har Homa building site in East Jerusalem and exchanged words with a local Palestinian MP, Salah Ta'amri.
Israeli officials understood that Mr Cook had agreed to visit the site with an Israeli escort, Danny Naveh, and meet Palestinian officials later in East Jerusalem. After the Cook-Ta'amri handshake, an Israeli spokesman told The Independent: "To use a British expression, that's just not done."
Heated consultations between Messrs Netanyahu and Cook were continuing in the Prime Minister's office last night. Israeli television reported that Mr Netanyahu was planning to telephone his opposite number, Tony Blair, and lodge a formal complaint.
British officials said they did not understood what the fuss was about. Mr Cook had merely shaken hands with a Palestinian. The encounter was, however, clearly premeditated - as a way to show the Palestinians that Britain had not succumbed to Israeli pressure. The intention was leaked in advance to the mass-circulation Tel-Aviv daily paper, Yediot Aharonot.
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