Lord Mawhinney was responding to a letter from Andy Burnham
The Football League wants the transfer window scrapped domestically and a transfer ban on clubs that fall behind on their tax payments.
Chairman Lord Mawhinney also wants to explore the possibility of a joint TV deal with the Premier League.
The plans were outlined in a four-page letter from Mawhinney to Culture Secretary Andy Burnham.
It was written in response to questions raised by the Government about football finances and the running of the game.
Burnham wrote to the Football Association, Premier League and Football League in October 2008, asking seven different questions.
The Premier League delivered its response earlier this week, outlining plans for greater financial transparency over the running of football clubs including a strengthened fit and proper person's test.
Mawhinney's letter was written following discussions with the Football League board and sent to Burnham on 18 May.
We are proposing their should be a distinction between domestic and international transfers
Football League chairman Lord Brian Mawhinney
In it Mawhinney argues that since Fifa "remain implacably opposed" to altering the current transfer window system, Government help would be needed if it was to be altered to allow domestic transfers.
But Mawhinney told the BBC: "We think the original idea was to regulate international player transfers.
"We are proposing there should be a distinction between domestic and international transfers."
When asked how likely he thought it would be that changes would be made to the transfer window, Mawhinney said: "I do not know the answer to that."
Currently the transfer window is open from 1 July to 31 August and from 1 to 31 January.
The proposals regarding tax and National Insurance payments are aimed at improving the relationship with Her Majesty's Revenue & Customs.
When a club is in administration it must pay in full its debts to its football creditors - a policy that is opposed by HMRC, which is no longer a preferential creditor and often has to settle for a greatly reduced offer.
Mawhinney said the Football League opposed scrapping its policy regarding football creditors.
But he added: "We will propose at our Annual Meeting next month an initiative which seeks to provide clubs with an incentive to keep up to date with payments to HMRC.
"If approved, clubs who fall behind will be embargoed from signing further players."
A new Football League television deal starts next season, with 10 live Championship games per season on the BBC.
The new agreements are worth £88m per season to Football League clubs and encompass terrestrial and pay television, broadband internet, video-on-demand and mobile services.
That deal runs until 2012, while the next Premier League deal starts in 2010 and ends in 2013, but Mawhinney is keen to explore the possibility of there being one deal in the future.
"It is not illogical to say is there a prospect of benefit to both if we turn it into one TV deal," Mawhinney told the BBC.
"The truth is we don't know the answer because we have never tried."
Culture Secretary Burnham has called for more consistency in financial regulations, more transparency and scrutiny of club ownership and debt levels.
He also wants rule changes for clubs in insolvency; a reconsideration of rules forcing insolvent clubs to pay football debts first and a strengthening of the fit and proper persons test for club owners.
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