McIlroy's comments came two days after PGA Tour Commissioner Tim Finchem cited the lack of data detailing specific advantages in anchoring and the 40-year history of long putters as the main reasons not to back the proposal.
"We've trusted this game of golf; we've put it in the hands of the R&A and the USGA for I don't know how many years, and we've always abided by the rules that they have set," McIlroy told a news conference on Tuesday at PGA National, site of this week's Honda Classic.
"I don't think this should be any different. I think golf is pretty good at the minute and it's in good hands.
Last November, the United States Golf Association (USGA) and the Royal and Ancient (R&A) proposed a ban on players anchoring putters to their body, saying they wanted to outlaw the practice by 2016 to help preserve the "skill and challenge" of putting.
Players and the golfing community were then given 90 days to discuss the proposal, a period which concludes at the end of this month.
Finchem, who was speaking during the WGC-Accenture Match Play Championship final at Dove Mountain, was far from clear over what would happen if the proposed change was implemented against the PGA Tour's wishes.
"I don't know, because we have, I think, carefully and intentionally avoided at this point getting into a discussion about that issue," said Finchem.
"Our regulations provide that we will follow the rules as promulgated by the USGA provided, however, we retain the right not to in certain instances if we see fit."
The USGA responded on Monday, saying that its 90-day comment period remains in place and that they expect to make a decision in the coming months.
The European Tour has not yet made a statement on the issue but on Tuesday the Daily Telegraph suggested it was not looking for a conflict with the rule making bodies.
While McIlroy has been in favour of a change he said he would not have a problem if pressure from the PGA Tour resulted in a climb down from the governing bodies.
"You are going to have a few guys that say they don't want (the long putter) and there's going to be guys that have used it their whole lives that say that they can't play without it," said McIlroy.
"If it were up to me I would just (follow) whatever decision the USGA comes to ... maybe the pressure that the PGA Tour has put on them might change their minds and (make them) rethink. And if they do that, then that's totally fine with me."
McIlroy also agreed with Ryder Cup-winning captain and eight-times European Tour number one Colin Montgomerie, who warned on Monday that Finchem risked dividing the sport.
"Monty said this divide isn't good for golf, and I don't think it is. I think we all need to be on one side or the other," said the Northern Irishman.
Three of the past five major winners have won with a long putter and McIlroy said that factor had pushed the issue into the forefront.
"It was a bit of a knee-jerk reaction to how much success people were having with it," said McIlroy.
"I'm all for people enjoying the game and trying to make the game as easy as possible and bringing people to the game, and if that means that they should allow belly putters or anchor putters to make it easier for the general public, then you know, that's a good thing.
"But then they talk about 'bifurcation' and whether you should have one set of rules for us and one set of rules for the amateurs; it's just a bit of a mess. It's just opened a can of worms with it."