Nanai had a night to forget in his side's 42-12 loss to Manly to open round one, with the 22-year-old clocking up more missed tackles (four) than runs (three).
The back-rower's spot has been taken by former Canberra forward Kai O'Donnell, who arrived in Townsville over the off-season following an impressive three-year stint with Super League side Leigh.
"Jeremiah is an elite attacking player but needs to improve some defensive parts of his game," Cowboys coach Todd Payten told the club's website.
"He's going to get some time in the Q Cup, which was not an easy decision but I felt it was important for the group that if we want to improve as a team, defence is first and foremost."
O'Donnell will make his Cowboys debut against Cronulla on Saturday, with Jason Taumalolo lurking in the club's extended squad as he recovers from a foot injury.
Cronulla have kept faith with the same side defeated by Penrith in Las Vegas.
The Panthers have been boosted by Brian To'o's return to fitness for Friday's clash with the Roosters, who will be without Victor Radley due to concussion.
In Friday's earlier game, the Warriors are unchanged for the arrival of Manly in Auckland.
The Sea Eagles have brought in Josh Aloiai for the injured Siosiua Taukeiaho.
On Saturday, Lewis Dodd will watch from the reserves bench as Jamie Humphreys retains his spot as Wayne Bennett's first-choice halfback and goes up against a St George Illawarra side guided by axed Souths half Lachlan Ilias.
Fletcher Myers and Bayleigh Bentley-Hape will replace Jack Wighton and Tyrone Munro respectively.
Elsewhere, Canberra made some minor changes to cover for the suspensions of Xavier Savage and Joe Tapine.
Albert Hopoate gets the nod in Savage's wing spot, while a forward reshuffle sees Englishman Matty Nicholson come on to the bench for his NRL debut.
On Sunday, Api Koroisau and Jahream Bula return to face Parramatta, while the Gold Coast will unleash a strong and powerful pack for their trip to face Canterbury.
Des Hasler has named Tino Fa'asuamaleaui, Mo Foutaika and Reagan Campbell-Gillard to start against the Bulldgos.
In Thursday's round-opening match, Adam Elliott comes on to the bench for Newcastle to face a Dolphins side boosted by the returns of Kodi Nikorima and Mark Nicholls.
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