ISRAEL’S defense minister and a Yasser Arafat envoy agreed Israeli forces would begin pulling out of parts of Gaza and Bethlehem to be replaced by Palestinian security. But the breakthrough was shadowed yesterday by opposition from Islamic militant groups.Israeli Defense Minister Binyamin Ben-Eliezer and Palestinian Interior Minister Abdel Razak Yehiyeh reached the agreement late Sunday after a three-hour meeting in Tel Aviv.Israeli Foreign Ministry spokesman Mark Sofer called the deal “a glimmer of hope,” but said Israel expected Arafat’s Palestinian Authority to rein in Hamas and other militants. Hamas spokesman Ismail Haniya said yesterday that his group would not stop its attacks. Islamic Jihad, another militant group, said attacks would continue.Israeli military commanders were scheduled to meet yesterday to determine how and when to begin the pullout. In the past, Israeli troops have waited until nightfall before moving, and they were expected to follow that practice in this case.If the initial pullback from Gaza and Bethlehem is followed by calm, the Israelis would return other areas to Palestinian Authority control.Nabil Abu Rdeneh, an aide to Arafat, said the Gaza and Bethlehem withdrawal would “prepare the atmosphere” for troop pullbacks in other Palestinian areas. Foreign Ministry spokesman Sofer, though, said no timetable had been set.The agreement was the first sign of progress toward peace in months.