The newspaper said it had received an independent account of how Jihadi John was injured and rushed to hospital after an air strike in Al Qaim, in Anbar Province, western Iraq.
The Foreign Office spokesman added: "We have a number of sources of information coming in.
"The incident occurred last weekend, and so we have received the reports in the last few days. We don't have any representation inside Syria, and so it is difficult to confirm these reports." The Foreign Office also issued an official statement saying: "We are aware of reports. We cannot confirm these reports."
A spokesman for US Central Command said they were unable to confirm the details for security reasons.
The joint US-Iraqi mission left at least 10 Isis commanders dead, and about 40 injured.
Those reportedly hurt included Isis leader Abu Bakr Al-Baghdadi.
But until now, Jihadi John's presence at the meeting had not emerged.
It is also not known whether Jihadi John was intentionally targeted or merely happened to be present.
The secret, heavily guarded meeting took place in a makeshift underground bunker beneath a house in Al Qaim. At least 30 tribal elders from various parts of Syria and Iraq gathered to pledge allegiance to Al-Baghdadi, according to the Mail's Syrian source. He said Jihadi John, as a senior Isis figure in his own right, who goes by the nomme de guerre Jalman Al-Britani, was also present.
According to the source, a nurse who treated the wounded in a hospital in Deir-ez-Zour confirmed that one of the names on the injured list was Jalman, saying it was "the one who slaughtered the journalists".
It is not clear how seriously the British fanatic was hurt, but the source said he and Al-Baghdadi were rushed to the Al Qaim General Hospital for treatment.
Isis members issued urgent calls through the local mosque's loudspeakers, appealing for residents to donate blood at the hospital.
The source added that Jihadi John, Al-Baghdadi and the other wounded Isis personnel were then driven to Syria, and travelled 320km north along the Euphrates valley to the Isis stronghold of Raqqa.
The injured were taken to two captured Syrian army barracks near the city in the hope that underground medical facilities there would provide protection against further air strikes.
The source said Jihadi John usually travelled in a black Audi jeep accompanied by six other British terrorists acting as his bodyguards.