The 26-year-old France international returned from a 12-week lay-off against Anzhi Makhachkala in Moscow last week, but has sat out the two games since and has now been told he may need an operation.
Manager Alan Pardew said: "Looking at him, I think he's going to need an operation on his hamstring, and it will probably leave him missing for the rest of the year, I think. We have had to absorb that in all the good news that we have had."
Ben Arfa tore his hamstring during a 2-1 Barclays Premier League defeat at Fulham on December 10 and spent a frustrating three months on the sidelines.
He was thrown straight in at the deep end at the Luzhniki Stadium last Thursday night when he was asked to play as a lone striker, and he had a glorious second-half opportunity to snatch victory.
However, he was unable to take his place in the squad for Sunday's 2-1 win over Stoke, and was ruled out of last night's return against Anzhi, which saw the Magpies book their place in the quarter-finals, by Pardew on Wednesday.
Now it appears his season could be over, and a man who spent all but four games of his first campaign on Tyneside recovering from an horrific double leg fracture, may have to turn his attention to August.
Pardew said: "That's the priority for him now because he's been a huge miss for us.
"He gives us that X-factor. In a game like last night's where he could open the door for us, we haven't got that luxury.
"Unfortunately for Hatem, that's the news that he didn't want to hear. But as far as we are concerned, the team has responded well in his absence and hopefully, we do that until the end of the year."
Meanwhile, Pardew confirmed that the groin problem with which Yohan Cabaye limped off last night is not too serious, and he could yet be involved at Wigan on Sunday.