While the Cylons are officially present only as "allies and friends of the legitimate Colonial government", they are in reality in complete control of the planet. The occupation authority attempts to rule by consensus, but as a copy of Number Three notes, the strains of occupation make consensus more difficult to come by. The Cylons also attempt to maintain control by working alongside humans in more helpful roles; at least one Number Six works in waste reclamation (TRS: "Faith"), and other Cylons assist human farmers in tending and harvesting crops (TRS: "Battlestar Galactica: The Resistance").
While all twelve Cylon models are on New Caprica, only the following members of the Significant Seven take part as the Final Five believe themselves to be human:
- Number One - At least two copies of Number One, under their name Cavil, are present, to the apparent chagrin of the other models—Cavil often mocks their faith and makes outrageous, potentially sarcastic suggestions, such as executing Baltar. Copies of Cavil also free Saul Tigh from custody, and Tigh's wife, Ellen, performing sexual favors upon another copy of Cavil in exchange for her husband's freedom. Cavil also supervises the attempted executions in "Precipice", after being left to die when the New Caprica Resistance frees the prisoners, this copy at least decides that the occupation is no longer worth it after being forced to kill himself and painfully download.
- Number Two - Only one copy of Number Two, under the name of Leoben Conoy, has been sighted, who is the same model interrogated by Kara Thrace in "Flesh and Bone". He holds Thrace captive and attempts to force her to live a married life with him. However, she kills him and forces him to download at least five times before finally appearing to give in. Conoy, interestingly, does not seem to be part of the Occupation Authority per se. For instance, he is never present on Colonial One, where the other Cylons discuss and decide the course of the occupation. He abducts a human child named Kacey Brynn, and claims that she is another hybrid child created from Thrace's ovary (TRS: "The Farm").
- Number Three - At least two copies of Number Three appear to be posted to the planet, one of which is the same copy that knew Caprica-Six and Sharon Valerii on Caprica. Three's role is largely supervisory, although she also begins a path of spiritual discovery on the planet that leads her to question her faith and discover that Hera, the child of Karl and Sharon Agathon still lives.
- Number Four - Number Four, also known as Simon, is sighted twice, voting with the others to agree on executing suspected members of the insurgency, and later relaying orders to Cylon forces on the surface of New Caprica during the uprising and exodus of the human population.
- Number Five - At least two, maybe three copies of Number Five are present on New Caprica. These copies are at times violent towards humans, supervising the temple massacre, shooting Caprica-Six, threatening Baltar at gunpoint, and suggesting that if the occupation fails, they could simply nuke the New Caprica settlements. At other times, the Fives seem optimistic about the possibility of lasting peace, convincing Jammer about the potential of both peoples working in harmony, and discussing with Gaius Baltar how small things, like the presence of sufficient toilet paper, would help to quell human unhappiness. A Five is shot by insurgents and is treated by Doctor Cottle despite being a Cylon. Cottle is able to save his life without him having to download.
- Number Six - At least four copies of Number Six are assigned to the occupation, including Caprica-Six. Caprica-Six has a different perspective than the other copies of her model, and is present largely to rejoin the company of her beloved Gaius Baltar. She, along with Boomer, is most optimistic about the possibility of lasting peace, and is reluctant to adopt stern measures. Another copy, seen in (TRS: "Faith"), worked at the waste reclamation plant with Jean Barolay who drowned her for being a Cylon despite this Six doing nothing to her. This leaves her with severe psychological trauma after she downloads.
- Number Eight - Sharon "Boomer" Valerii is present on New Caprica, as is at least one other copy of her model. Valerii is not in favor of the detentions and executions but has does not make a stand on these issues, probably because the others are already well aware of how she feels without needing to be told and because of what happened to Caprica-Six when she dissented openly. She also apparently loses her influence over the other Cylons as the occupation continues as she is unable to get Cally Tyrol out of detention or off a death list.