According to Palestinian sources, Israeli Defence Minister Shaul Mofaz telephoned Palestinian Authority (PA) Interior Minister Nasr Yusuf on Saturday night, apologising for the incident.
Mofaz reportedly urged Yusuf to ensure that the killings remained a "localised incident" and not to let it wreck the uneasy calm in the occupied territories.
Earlier, an Israeli army spokesman told Aljazeera.net that the three teenagers killed were "armed smugglers".
However, Palestinian officials said the teenagers were playing football outside the Rafah refugee camp at the southern edge of the Gaza Strip.
The killing by soldiers manning an army watchtower infuriated Palestinian resistance groups as well as PA leaders, who have accused Israel of wantonly violating the ceasefire.
PA President Mahmud Abbas described the incident as a "murderous act" that constitutes a "brazen violation of the calm".