Benitez, who had earlier accused United counterpart Sir Alex Ferguson of hypocrisy and serial whingeing, returned to the fray to point a finger at Gill, a senior figure at England's governing Football Association.
"Is there a conflict of interest with David Gill at the FA?" asked Benitez, whose side could be overtaken by United at the top of the Premiership if the Red Devils win their two games in hand against Wigan and Bolton.
"That is another fact. It is a fact that one person has a lot of power and control, and is on a lot of committees in the FA. To me that is very strange."
But Gill, who was in Macau to launch details of Manchester United's 2009 tour of Asia, dismissed the comments as "pretty irrelevant in the grand scheme of things."
"I was elected over the summer by the Premier League clubs. I'm very clear in my role," he said.
"I think it is totally incorrect to assert that," Gill added, referring to the conflict of interest accusation.
"It's not how I work. I do not think I would have been elected for the last two years if that was the case. He missed the boat completely."