An eight-year Professional Game Partnership was announced on Wednesday by the Rugby Football Union, Premiership Rugby and Rugby Players' Association that sets out how the game will be run.
The RFU will pay the 10 Premiership clubs £33 million per season for the first four-year cycle, with a profit share dictating the funding for the second four-year cycle.
As part of the arrangement, Borthwick will have the freedom to select up to 25 players who will be paid as much as £160,000 annually in return for greater control of how they are managed on club duty.
This includes deciding on medical issues such as when a player undergoes surgery, potentially affecting his availability for club matches and thereby leading to possible flashpoints with directors of rugby.
The RFU said the new system would "ensure optimum preparation for key international fixtures".
"The England national team benefits by having control over the individual development programmes, medical and S&C (strength and conditioning) of the best players in England at the peak of their form and in the best shape to play for their country," said RFU chief executive Bill Sweeney.
"This eight-year commitment will reshape the rugby landscape and reset the professional game to support, showcase and fund our game for the next decade and beyond."
While Borthwick will not be able to dictate selection for fit England stars on hybrid contracts when they are playing for their clubs, medical decisions he makes could affect their availability for Premiership and European matches.
Exeter boss Rob Baxter has expressed concerns over the arrangement.
"My concerns are around how the medical intervention part works. The proof of the pudding of this agreement will be down the line," he said.
"If we look in two or three years and they are all playing England games and not playing club games, the clubs will say that outcome doesn't work for us. None of us will know until we get down the line."
