Prison officers are using colour-coded cards on cell doors to highlight which gang members must be kept apart.
Speaking at the Prison Officers' Association (POA) conference, assistant general secretary Gabriel Keaveney said the number of prisoners on protection is rising.
"In some cases it gets so problematic that you have to put a different colour card outside their door," Mr Keaveney told delegates in Galway.
"So the reds can mix with the blues and not the yellows. The greens are OK with the blues and not the rest. It's insane.
"You also have people who were never in prison before come up to the gate and say, 'I'm with X or Y. I'm from this part of the city'."
Mr Keaveney also told of how gang bosses have lieutenants operating on their behalf in prisons.
"If you have gang leaders in a place, they will have influence over a wing or a landing or a block," he said.
"The influence they have is huge, so you have to segregate them."
In response, the Irish Prison Service conceded that the increase in recent years of organised gang activity in the community has had significant implications for the management of prisons.
"The people leading or associated to these groups have been identified, targeted and profiled," he said.
The POA also raised the issue of having to deal with fights between prisoners, and increasing attacks on officers, with no batons or pepper spray to help them.
"When two prisoners are fighting with blades, what do we do?" said Mr Keaveney.
"We have to go in with our sleeves twisted up and talk to these people."
The Irish Prison Service said the recent State Claims Agency report on assaults on prison staff by inmates did not recommend the issue of batons.
The agency said it felt the sight of officers carrying batons in prisons could do more harm than good.
However, batons have been issued to staff while on escort duty.