Ayoub manages Australian-based Kiwis Jordan Rapana, Sam Moa and Sam Tagataese who are with Canberra, the Sydney Roosters and Cronulla respectively.
Australian media are reporting the police investigations are related to the Parramatta salary cap dramas and there is no suggestion other players who are with the agents in question but don't play for the Eels are being investigated or have done anything wrong.
Officers from the NSW Fraud and Cybercrime Squad carried out search warrants at homes in the Sydney suburbs of Leichhardt, Woollahra, and a business premises in the CBD, police officials said.
No arrests are expected, but officials confirmed the searches were being conducted in relation to Strike Force Rhodium, the unit tasked with investigating salary cap breaches at the Eels club.
The raids are the latest incremental shift in a probe that was prompted by an award-winning series of articles about alleged salary breaches first published by The Sydney Daily Telegraph.
Detectives were seen entering the Woollahra home of Beavis, a manager to former Eels player Jarryd Hayne, about 9.30am. Concurrent raids were taking place on the home of Ayoub, officials said.
Comment is being sought from both men.
An official said the operation had been planned and was largely being carried out to seize documentation.