During Israel's 1982 invasion of Lebanon, Hobeika was the liaison officer to Mossad. On 15 September, following the assassination of President-elect Bachir Gemayel the previous day, the Israeli army took over West Beirut. Minister of Defence Ariel Sharon and Chief of Staff General Raful Eitan had decided that the Israel Defense Forces (IDF) would not enter the Palestinian refugee camps but this task should be undertaken by Lebanese Christian militias. On the night of 16 September 1982, Hobeika, was on the top floor of the Israeli forward command post, when the first 150 militiamen entered the Sabra and Shatila camps, which had been evacuated by the Palestine Liberation Organization (PLO) at the beginning of September. Two hours after the first Phalangist force entered Shatila, one of the militiamen radioed Hobeika asking what to do with 50 women and children they had taken prisoner. Hobeika's response was overheard by an Israeli officer, who testified that Hobeika replied: "This is the last time you're going to ask me a question like that; you know exactly what to do." Other Phalangists on the roof started laughing. Brigadier General Amos Yaron asked Lieutenant Elul, Chef de Bureau of the Divisional Commander, what the laughter was about and Elul translated what Hobeika had said. Yaron then had a five-minute conversation, in English, with Hobeika. What was said is unknown. Over the next three days, the LF killed between 762 and 3,500 residents of the camp. Until 1985, Hobeika sided with Israel. However, then he began to support Syria's presence in Lebanon.