The SPFL has cited "factual inaccuracies" by six Premiership clubs who questioned the autonomy of an independent review into governance.
Rangers, Aberdeen, Livingston, Motherwell, St Johnstone and St Mirren expressed "serious concerns".
The group are seeking "full clarity on numerous issues" to "determine if further action is necessary".
The league body says it will discuss the report's recommendations with all 12 top-flight clubs.
The SPFL said: "We can confirm that yesterday we received a letter on behalf of six Premiership clubs. The letter contained a number of factual inaccuracies, which we have now addressed with those clubs.
"We look forward to discussing the recommendations of the independent governance review with all Premiership clubs at a meeting soon, once the process has been completed."
Clubs say statement 'did not reflect full findings of report'
An independent review of the league's operations was commissioned in July after SPFL chairman Murdoch MacLennan apologised to Rangers as a dispute over sponsorship was concluded.
On 22 January, the governing body announced that a draft report showed it complies "with significant elements of the UK Code of Corporate Governance", with MacLennan saying: "I am reassured but not complacent."
The six clubs say that statement was issued without "the approval or knowledge" of league members, adding that it "did not reflect the full findings" of the report.
"The SPFL board is to meet at a future date to discuss the draft report's contents, making it highly inappropriate for the SPFL chairman to have made any public comment ahead of that meeting," added the co-signed complaint.
"Regarding the report itself, the clubs and others are deeply concerned about its independence, given that the SPFL executive received the first draft of the report and made changes to it prior to sending it to SPFL board members.
"Of the 42 member clubs, only one had the opportunity to input into the report's investigation, outside of current or previous SPFL board members.
"Despite several requests from the clubs, the report has yet to be released to any of the member clubs, despite the clubs footing the bill for its creation.
"The handling of the independent governance report has brought the clubs' governance concerns to a head, and it is now incumbent on the SPFL board and executive, for the sake of trust in those running our game, to provide clarity over these clear and deeply troubling concerns as a matter of urgency."