The multi-million pound deal between the Rugby Football Union and Premiership Rugby is set to make Sam Underhill unavailable for selection.
Underhill, who plays for the Ospreys in the PRO12, apparently would have to leave the region in order to be eligible to represent England.
The new deal which was announced on Monday says that the "exceptional circumstances" rule is now solely due to an injury crisis, meaning that if the former England U18 flank wants to play for his country at senior level he would have to switch to a Premiership club.
"When we wrote the first agreement it was always injury related, we just never wrote it in as specific as that,” Premiership Rugby chief executive Mark McCafferty told The Telegraph.
"We have clarified it only in the sense of writing what we had in mind eight years ago. If you get big injuries ahead of playing a tier-one country – maybe the next in line is inexperienced and almost to a point of safety issues. Under those circumstances that would definitely be exceptional and you might have to look elsewhere."
RFU chief executive Ian Ritchie added: "We discussed it again with Eddie (Jones) and we agreed with the exceptional circumstances clause and it is left where it is.
"I think everybody is clear and Eddie is very good at communicating it to players. We think it is a good clause and the right clause."
The new deal is set to see England increase their Elite Player Squad from 33 to 45 and also give head coach Eddie Jones greater time with his players, with a two-day camp scheduled before the Premiership season kicks-off and another in early October before the November Tests.