Jamie Ginn, 50, was arrested about 1pm on Tuesday and charged with drug and firearm offences.
WA Police say six hours later, he suffered a medical episode in his cell in Perth watch house.
Ginn is believed to have suffered from a seizure, though WA police would not confirm details of the events surrounding his death.
"At this stage, it's a medical episode, there will be a post-mortem and that's what that's there for," WA Police Commissioner Col Blanch said on Wednesday.
Ginn was not unresponsive when police came to the cell and it is unclear whether he died before paramedics arrived.
"Police immediately responded within minutes, he wasn't unresponsive at that time, but they were giving medical aid to him for some time," he said.
Mr Blanch said he hoped there would be no adverse reaction from the bikie community in Perth.
"(A) transparent investigation will certainly determine whether or not we acted appropriately - as it should," he said.
"But I don't think there's any real blame to be put on anyone."
The death is not being treated as suspicious and a report will be prepared for the coroner.
Police Commissioner Col Blanch said senior bikies would continue to be targeted by police.
Ginn's arrest was part of a recent crackdown by WA Police on bikie activity in Perth after an increase in activity in the region.
Police said members of motorcycle gangs must adhere to the regulations.
"Those in outlaw motorcycle gangs that decide to take on the roles of president or vice president ... you will be subjected to significant legal provisions like the firearms prohibition order and you will be the target of police, there is no doubt about it," Mr Blanch said.
WA Premier Roger Cook said he believed Ginn died of "natural causes" and that he was not concerned about growing tensions in the bikie community.
"The presence of bikie gangs continues to be a concern for everyone in Western Australia," he said on Wednesday.
"But we can have confidence that the police respond both on the basis of intelligence and activity."
The newly appointed bikie boss was convicted of displaying outlawed bikie insignia in March after new laws were introduced in 2021.
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