The Premier League wants Manchester City to take Liverpool's vacant slot in the Uefa Cup after they were handed a place in the Champions League.
League chiefs reacted angrily after Uefa revealed City would not be able to step in as a replacement for Liverpool.
They believe an English Uefa Cup place has now been taken away.
A spokesman said: "We will be asking the FA to formally re-nominate Bolton, Middlesbrough and Manchester City in the three Uefa Cup places allocated."
The League is also unhappy that Uefa has insisted that Liverpool must share in the cash pot awarded to England's four other Champions League entrants - Chelsea, Arsenal, Manchester United and Everton.
The spokesman added: "We are very pleased for Liverpool and in many ways Uefa has taken a brave and correct decision.
"However we do not feel this should have been at the expense of the English game's third Uefa Cup place, nor the Champions League pool as distributed between the four qualified clubs."
Football Association chief executive Brian Barwick admitted he felt there was little hope of Uefa backing down over City's Uefa Cup place.
"We have lobbied for Manchester City during the process while we've been lobbying for Liverpool," he told BBC Radio Five Live.
"But Uefa have capped the number of teams at seven, going to the two European competitions - other than through the Intertoto or the fair-play and, therefore, it's unlikely that the door will be opened."