"I believe that Madrid and Barcelona are receptive and are ready to be more flexible in the sharing out of [income from] rights," Wert was quoted as saying in Wednesday's edition of As sports daily.
He also warned that if media firms were unwilling or unable to continue paying current prices for rights, which are one of the principle sources of income for football clubs, "the situation for football will be difficult".
Barca and Real did not immediately respond to a request for comment.
Clubs in La Liga negotiate their TV deals individually, unlike other major European leagues which have systems of collective bargaining, and Real and Barca take about half the total pot of around 641 million euros.
Research published in April by Jose Maria Gay, a professor of accounting at the University of Barcelona, showed that in the 2010/11 season Barca reaped 163 million euros from TV rights, Real earned 156 million, while Valencia earned 42 million.
The disparity in wealth means the big two's domestic rivals struggle to afford the best players or meet their wage demands and have no chance of challenging for the league title.
Valencia, who finished third last season, were 30 points behind second-placed Barca and 39 behind champions Real.
Introducing a system of collective bargaining similar to the one used in the English Premier League would level the playing field and help prevent clubs racking up unsustainable debts, analysts have said.
Spanish clubs had combined debt of some 3.53 billion euros in the 2010/11 season, Gay's research showed.
Clubs owe a total of 763 million euros to the tax authorities alone and Wert told As he was confident a recent agreement under which those debts would be paid off over time would resolve the problem.
"We are in a very difficult liquidity situation," Wert said.
"I do not believe that any club will fail to meet its obligations and that the situation will be resolved relatively rapidly," he added.
"The professional football league (LFP) is very committed and very active in the preparation of the protocol and I believe the clubs will meet their obligations scrupulously.
"But it has to be regulated by the sector itself."
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