The France international was out for 12 weeks before making a comeback against Anzhi Makhachkala in the first leg of the Magpies' Europa League tie, but aggravated the injury during the match.
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"He needs an operation on his hamstring and he could miss the rest of the year," Alan Pardew told reporters.
"It is terrible news. Hatem gives us the x factor and will be a big miss."
However, Pardew did have better news regarding Yohan Cabaye, who he says has "half a chance" of playing against Wigan on Sunday afternoon.
Newcastle defeated Anzhi thanks to a 93rd-minute winner from Papiss Cisse, and have drawn Benfica in the quarter-finals of the Europa League - a tie Pardew is positive about winning.
"It's a great draw for us," the manager told the club's official website. "The Estadio da Luz is a great venue. I've been there and it's a fantastic stadium.
"Importantly, we are at home in the second leg and that will give us an advantage. I'm sure we will have a full house for that.
"After what the stadium was like last night [against Anzhi], I know it will be another brilliant atmosphere, and let's hope we can bring a result back from Benfica in the first leg."