McGuire was quoted in News Ltd newspapers on Tuesday suggesting the COLA had given the Swans an unfair advantage by allowing them to recruit Kurt Tippett and Shane Mumford.
The Collingwood president clearly felt that duo were the match winners against the Western Bulldogs on Sunday.
"I have always argued the opportunity to succeed comes from being successful on the ground and that involves getting rid of the perversions in the draft and salary cap," McGuire said.
"You only have to look at the weekend. The Bulldogs were in the game against Sydney and then (Shane) Mumford and (Kurt) Tippett went berserk.
"Take them out of that side and put Callan Ward and Jarrod Harbrow in for the Dogs and it is a different story.''
Ward and Harbrow both left the Bulldogs for Greater Western Sydney in 2011 and the Gold Coast in 2010 respectively.
The COLA, which is worth in the region of $900,000 per year to the Swans and Giants, has been a recurring point of contention between the Sydney clubs and the rest of the competition.
Many public comments were made during the Swans' recruitment of Tippett, stating the COLA had directly allowed them to add a high-priced key forward to a flag-winning line-up.
The Swans have regularly bristled at that suggestion.
Last year, they offloaded six players – Mark Seaby, Jarred Moore, Trent Dennis-Lane, Matt Spangher, Brett Meredith and Nathan Gordon – freeing up around $1 million in cap space.
It's understood the club also privately feels McGuire overlooked facts such as that Kieren Jack, an unwanted teenager who was given a shot on the Swans' rookie list back in 2005, was actually voted by both coaches as the best player on the ground on Sunday, not Tippett or Mumford.
On Tuesday, Longmire felt confused by McGuire's latest outburst.
"I'm not sure why Eddie brings that up," he said. "Because if the cost of living allowance wasn't here for GWS and Sydney, we'd actually be behind the eight-ball.
"There's plenty of research that suggests the cost of living in Sydney is actually a significant cost and I'm sure that Eddie has been talking about having an even playing field.
"Well if it wasn't for the cost of living, it wouldn't be an even playing field for GWS and the Swans."
McGuire's comments come after he and a number of club and AFL officials met with executives from the NFL, NBA and MLB in the United States to discuss equalisation.
In relation to on-field matters at the Swans, Longmire said injured trio Adam Goodes, Lewis Jetta and Sam Reid may not be fit until the first week of the finals.
There is likely to be one change to face Collingwood this week, with Ben McGlynn now free to play after serving a three-match suspension.
Longmire has been thrilled with how his young brigade has been performing, but suggested one is likely to miss out.
"Benny (McGlynn) is still our leading goalkicker and has been a real pressure forward for us before he got suspended," he said.
"He's a quality player who's good offensively and defensively in our front half.
"We've been fortunate that the younger kids who have come into the group during this eight, 10, 12-week period when we've had some injuries have done a really good job for us.
"We've got plenty of faith in them being able to continue to do a good job against quality opposition.
"This week one of the players might be a bit unlucky to miss out, but it's not unusual."
James Dampney is a reporter for AFL Media. Follow him on Twitter @AFL_JD
