Clarke and Jacobson are both set to miss the same amount of time with a high ankle injury and thigh injury respectively.
Hotham will likely miss the entire Rugby Championship as he requires surgery for a high ankle sprain, which will open up a third halfback spot – with no obvious name to fill the void.
Coach Scott Robertson could turn to Finlay Christie, who hasn’t played for New Zealand since the second test against England last year.
Reports over the weekend have linked the 29-year-old with a move to England and Premiership side Newcastle and if he does make the switch, Christie could end up playing for his country of birth, Scotland, at the 2027 Rugby World Cup.
Another option is Folau Fakatava, who last played for the All Blacks in 2022.
Meanwhile, eight players who featured in the 3-0 series sweep over France will be released to play in the opening round of the NPC.
Waikato will have midfielder Anton Lienert-Brown for the opening game of the season against Auckland on Thursday.
Wellington and Canterbury will have Ruben Love and Brodie McAlister, respectively, while Christian Lio-Willie may feature for Otago when they take on Southland.
Emoni Narawa and Pasilio Tosi are in contention to represent Bay of Plenty, while Timoci Tavatavanawai and Dalton Papali’i could feature for Tasman and Counties Manukau respectively.
Ben Francis is an Auckland-based reporter for the New Zealand Herald who covers breaking sports news.