The idea of the top clubs having feeder sides or even 'B teams' in the lower leagues has emerged this week, with the plan seemingly being to take it to the commission being set up by FA chairman Greg Dyke.
Clarke is concerned the plan has been mooted before the commission has even met, and has warned against the commission's work being damaged by self-interest from English football's different groups.
He told Press Association Sport: "The Football League is not keen to have feeder clubs. If you look at leagues which do have them, you tend not to get good attendances.
"We don't like the idea of it and I don't believe it would solve the problem - but we will look at it as nothing is off the table.
"But if there is a proposal it should be put forward as part of the process and be dealt with by the commission.
"Let's not hijack Greg Dyke's process, let's get all the ideas on the table without everyone having personal agendas and having the process degenerate into being parochial, (and characterised by) tribalism and faction fighting.
"That's how we got into this mess in the first place."
He added: "We have to put parochial self-interest aside and do the right thing for English football and its fans, and forge a way ahead together."
The system of feeder clubs is common on the continent - for example Barcelona B play in the second tier of Spanish football but cannot be promoted. Those responsible for youth development at Premier League clubs believe more formal relationships with lower league sides would help the development of players aged 17 to 21.
Clarke said the lack of young English players coming through to the top of club football was close to a crisis point.
He added: "If you are on a boat that's sinking it all seems fairly academic until the water starts reaching your nostrils.
"The issue is how we have the best club football in the world and a competitive England team. We need to understand the trade-offs and the compromises that need to be made to allow us to have both rather than one or the other.
"Nobody wants to kill the Premier League, it's a wonderful product with worldwide success, what we want to do is have a top-class England team as well."
The Football Supporters' Federation insisted there would be a major backlash by fans to any feeder club system in England.
An FSF spokesman said: "This idea comes around every couple of years and the overwhelming majority of fans are absolutely opposed to it. The backlash would be huge.
"The English league system is one of the strongest in the world and that shouldn't be jeopardised. No other country has such big crowds going down to the fourth and fifth tier.
"We don't think it's just fans of Football League clubs who are against this either, we think most fans of top-flight clubs will too. Every club has its own identity, however big or small.
"Back in January 2012 we polled our members on this very subject and 86 per cent said they opposed the idea of top-flight clubs buying feeder sides."