The Federal Court ruled Queensland Police actions breached the Racial Discrimination Act after riots were sparked following the death of an Indigenous man in custody on the island in 2004.
Mr Wotton, who was jailed for inciting violence, was awarded $220,000 along with his family as part of the judgment.
However, the Queensland Police Service and the state government appealed the decision soon after, in a move which has been slammed by indigenous elders as perpetuating racism and extending the hurt caused by the saga.
Mr Wotton's lawyers released a statement on Wednesday saying he has mixed feelings about accepting the payout money.
"We'll accept the payment because the court has ordered it," Mr Wotton said in the statement.
"But thirty pieces of silver can't wash away the trauma which police caused to blacks on Palm Island twelve years ago."
Indigenous health campaigner Professor Gracelyn Smallwood launched a petition against the appeal which has so far gathered over 17,000 signatures.
"The state government and police still do not want to help, they just want to subdue Indigenous people," Prof Smallwood said in a statement.
Premier Annastacia Palaszczuk last week said she couldn't comment on the matter because it was before the courts.
"The government lodged the appeal. We are now letting the matter take its course," she said.
Ms Palaszczuk’s comments come amidst widespread criticism of the government's appeal, which has been slammed by Palm Island Mayor Alf Lacey and three north Queensland MPs.
The appeal will likely be heard in May.