The suspects were said to have been arrested in Sagamu, Ijebu Igbo, Emuren, and Ago Iwoye.
The attack on the two communities on Wednesday left about 11 persons dead.
The state Police Public Relations Officer, Muyiwa Adejobi, said 17 out of the suspects were arrested at Emuren axis while the remaining ones were nabbed at Ijebu Igbo, and Ago Iwoye.
Adejobi, a Superintendent of Police, said the state command also got information that the Aye Confraternity members were mobilising to storm Sagamu again on Friday.
He said the command instructed the Divisional Police Officer in Sagamu and his men to mount security checkpoints on the Sagamu-Ijebu Ode highway.
He said the command also had a hint that some traditional rulers in the affected communities were aiding and promoting the cult groups, warning that any of them found culpable would be dealt with according to the law.
He also warned that the command has zero tolerance for cultism and would do everything to nip their activities in the bud.
He recalled that the cause of the fracas was the killing of a goat of a rival group that was preparing for a festival.
He said, “On Wednesday, one of the cult groups went to go and kill the goat meant for a celebration by the other rival group. And they went angrily to attack them back but they have their target.
“The command did not have the record of those killed, they are hurting themselves and they have their targets, and at least to an extent we thank God they have not been killing indiscriminately.
“But today we have information that some of them are not from that community, they were invited to Emuren community.
“We have allegation that some traditional chiefs are harbouring them, and promoting them. We are going to spread the scope of our investigation to unravel this and if it is true, any community leader that is involved in promoting cultism will be dealt with according to the position of the Constitution. He will face the wrath of the law.
“We have 12 suspects from that angle. In Emuren alone, we have three suspects, they said one of them is a son to a chief, we are still investigating. We have Faleke Sultan, in the other community. We went on all-round operation, we have additional 12 just for today, making 17 suspects.
“In Emuren specifically which is the conflict theatre, we have Ismail Ali, sodiq Ibrahim and Ahmed Rafiu.
“We are working on them and we are going to subdue them, is not only in this place, all together in the state now we have arrested 40 suspects, spanning across Sagamu, Emuren, Ijebu Igbo, and Ago Iwoye.
“In Ago-Iwoye, we have arrested 17and as I speak with you we have information that they are coming again with their new boss to attack Sagamu, the DPO of Sagamu is on the Expressway now, they have blocked all the entrances into Sagamu.
“They want to cause problem and unrest for us in Ogun State and we are going to tackle them.”
The suspected members of the Aye Confraternity were said to have gone on rampage around 11am on Wednesday to commemorate their anniversary tagged 7/7.
The grand finale of the anniversary was reportedly held on Thursday July 7, 2016 at Emuren, a neighbouring community to Sagamu.
The hoodlums, numbering about 25, it was gathered, came from Emuren, wielding guns and machetes.
Their targets were said to be members of a rival cult group, Eiye Confraternity. The bandits, who were said to have wore masks, shot three welders at a border bordering Emuren and Igode.
They had mistaken the welders who were returning from work site on a motorcycle, as members of the rival cult group.
The rampaging cultists reportedly proceeded to the Fakale community, where they opened fire on a crowd watching a football match in a viewing centre, killing seven persons.