The plans were passed by a margin of 46 to 22 at Thursday's meeting of the Football League clubs at Walsall's Banks' Stadium, with three no-shows and one abstention.
The new system will increase the amount of coaching contact time for players in the country's top academies, those granted category one status, and Clarke told Sky Sports News: "We had a vote and it was strongly supported - the national game is behind developing better talent for the national side."
Payments to clubs for youth development will increase but the regulations also include the abolition of the transfer tribunal system, to be replaced by a fixed level of compensation - leading to fears that lower-league teams will lose their top young talent to bigger clubs on the cheap.
And Clarke added: "There's two aspects to it, there's the Elite Player Performance Plan which is pretty uncontentious really, a lot of good work done by a lot of people.
"Then there's the compensation plan, which determines how much large clubs pay smaller clubs for youth talent at different ages, and it's important clubs knew what they were signing up for and that each club had to decide whether they would be better or worse off financially under the new scheme."
The new tariff approach to transfer fees for young players will see an end to deals such as the initial ?600,000 fee that took 16-year-old Luke Garbutt from Leeds to Everton in 2009, or 14-year-old MK Dons starlet Seyi Ojo's proposed ?1.5million switch to Chelsea which was reportedly agreed this week.
Clubs will be paid ?3,000-per-year for every year of a player's development between the ages of nine and 11. The fee per year from 12 to 16 will depend on the selling club's academy status within the four-tier system, but ranges between ?12,500 and ?40,000.
The Dons also received ?2.5m from West Ham for forward Sam Baldock this summer, but chairman Pete Winkleman is behind the proposals, telling Sky Sports News: "Elite Player Performance is making sure we can develop players through the Football League, through the Premier League, for the benefit of our national team, and that was at the forefront of everybody's mind.
"Of course there are differences of opinion over how you might be able to do that, and there's lots of commercial things that people have to think about, but I think the really positive thing that comes out of today and really out of this whole re-look at youth development, is just how important it is for the future of football in this country that we get it right."
Source: PA
Source: PA