An MRI scan carried out after his arrival in Israel on Tuesday, when he told national team staff of the pain he was experiencing, revealed the true extent of the injury which was originally thought to be just a calf muscle injury.
"He arrived from Chelsea on Tuesday morning complaining of pains, the team doctor sent him for a scan and it revealed a significant tear. He did not train while he was here," national team spokesman Gil Levanoni said.
Benayoun's injury was described as a "hefty blow to the national team... he could be sidelined for months" on the Israel Football Association website.
Benayoun, 30, a vital component in Israel coach Luis Fernandez's plans, was already a doubt for the games against Croatia in Tel Aviv on Saturday and Greece in Athens next Tuesday because of what was thought to be a calf injury.
Benayoun suffered the injury in Chelsea's 4-3 League Cup defeat by Newcastle United at Stamford Bridge on September 22.
"I arrived with hope of helping the national team but unfortunately this is not a simple injury... an additional test will reveal what needs to be done," Benayoun was quoted as saying on the IFA website.
The Israeli joined Chelsea in July after spending three seasons with Liverpool and has scored one goal this season.
The IFA said the Israeli would travel back to England in the coming days to assess if he requires surgery.
Benayoun scored a hat-trick in Israel's opening Group F qualifier at home to Malta which they won 3-1 and played in the goalless draw against Georgia in Tbilisi.
Croatia are top with four points ahead of Israel on goal difference after two matches. Latvia are third with three points, while Georgia and Greece have two and Malta are bottom without a point.
