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Cooper, who shares the same manager as his friend Williams, won his first professional fight with a first-round knockout of an insurance company agent earlier this month, a week before his Super Rugby season-opener for the Queensland Reds.
"Do I like the fact that one of our Super Rugby players had a boxing match the week before the first game? In all honesty, no, not particularly," Pulver said in comments published by The Australian newspaper.
"Had I been coach of that team, that would not have been my preference. But that's water under the bridge. There's nothing I can do about that.
"My preference is those players who are contracted to the ARU focus on rugby."
New Zealand-born Cooper was ineffectual in the Reds' 24-6 loss to the Canberra-based ACT Brumbies at the weekend and gifted his opponents a last-minute try with an intercepted pass.
The 24-year-old's first fight, on the undercard for Williams's bout with South African Francois Botha in Brisbane, was held as the Reds lost 20-8 in a pre-season match to the Chiefs, last season's Super Rugby champions.
"Once I go into the ring there's all the lights, all the cameras - that's where I want to be," Cooper said after his first foray into the ring, adding that he hoped to have another fight later this year.