Mal Brough, Australia's Aboriginal affairs minister, said "I would urge all those with an interest in the case to accept the decision of the court calmly."
The verdict also raised questions about Australia's commitment to nearly 340 recommendations of an independent judicial inquiry in the late 1980s into how to prevent aboriginal deaths in jail.
Only one group of five police have previously faced court over the death of an Aborigine in jail.
They were acquitted in 1984 over an incident in Western Australia.
Michael Cope, president of the Queensland Council for Civil Liberties, said: "People shouldn't be arrested simply for abusing police."
A report this month showed Aborigines were 13 times more likely than other Australians to go to prison, while black youths were 23 times more likely to be detained.
Judge Peter Dutney of Townsville supreme court told the 12-member jury not to worry about the possible ramifications of the trial and consider only the evidence given to the court.
He said: "This trial is not concerned with police in general, it is not concerned with the riots which occurred after Mulrunji's death."
Medical experts told the court that Doomadgee's injuries could have been caused by Hurley falling on him by accident.
Hurley had pleaded not guilty to murder, but last week admitted he must have fallen on top of Doomadgee in a scuffle.
The police union, which backed Hurley, said it was trying to keep tensions as low as possible after the trial.
Gary Wilkinson, Queensland Police Union president, said: "There will be no celebration, there are no winner."