They are asking all member clubs to submit their own policing bills over the last two-and-a-half seasons to see how they compare with the demands of GMP.
And once that information has been gathered, league officials hope to sit down with the police and reach a compromise.
News that the league are getting involved comes as Latics ready themselves for their highest crowd of the season against Leeds on Saturday.
The club are hoping for a gate of at least 15,000 for the all-ticket clash, with Leeds having sold around 5,000 of their allocation.
Latics chief executive Brenda Spencer said: "There has been no further progress regarding our dispute with GMP but we do remain hopeful that the situation will be resolved in the near future.
"We are very grateful that the Football League are now looking into this matter and they have written to all member clubs to do a survey of policing costs over the last two-and-a-half seasons.
"This survery should help the league examine the treatment we've received and the charges we are being asked to pay in relation to our fellow clubs.
"At no point have we refused payment to GMP for the fine service they provide, we just feel we are being charged significantly more than some of the other clubs.
"All we are asking for is consistency and we are standing our ground.
"Dave Whelan has asked me to place on record his thanks to Sir Brian Mawhinney and the Football League for their involvement in helping us to try and resolve this ongoing dispute by looking into it in some detail.
"We will be co-operating fully with the League so that the facts of the case are present and open from our point of view."
It's hoped that the other clubs act speedily in supplying their own policing costs in order to get further negotiations with GMP going.
Spencer said: "When the survey is completed the league will request a meeting with the police in a further attempt to resolve this dispute.
"We are keen for this to be satisfactory resolved as soon as is humanly possible."
Latics and the police have been at loggerheads for some time now about the costs of police stewarding at games.
But it was only last month that the club went public in an attempt to get their side of the dispute across.
Figures produced by chairman Whelan show that Bolton who also fall under the GMP authority, were charged far less even though their crowds were twice and sometimes three times the size of Latics.
Fellow Championship sides Burnley and Preston, policed by Lancashire, were also charged considerably less.
On the playing front, a second-half goal from David Graham secured Latics Reserves a 1-1 draw with Walsall at the Robin Park Arena yesterday.
Graham is likely to be on the bench on Saturday against Leeds, who were keen to sign him in the summer before his switch to the JJB.
Andreas Johansson stepped up his bid for match fitness by playing all of yesterday's game, as did Jason Jarrett, and both can expect be among the substitutes this weekend.