Bayern Munich have been the most vociferous critics after their Dutch winger Arjen Robben returned injured from the tournament in South Africa. He has yet to play for the Bavarian club this season.
The biggest payout of $866,267 goes to Barcelona, followed by Bayern Munich ($778,667), Chelsea ($762,667), Liverpool ($695,600) and Real Madrid ($678,133), FIFA said.
European clubs took the lion's share with English clubs receiving $5,992,533 between them.
The amounts are based on the number of players each club sent to the World Cup and on the number of days spent at the tournament.
"We are pleased that we can share the success of the 2010 FIFA World Cup with the clubs by providing them a share of the benefits of our flagship event, in particular to recognise their efforts in the development of young players", president Sepp Blatter said on the FIFA website.
FIFA added that the total would rise from $40 million to $70 million for the 2014 World Cup in Brazil "to recognise the important part clubs play in the success of the World Cup."
But Bayern chairman Karl-Heinz Rummenigge, who is president of the European Clubs' Association, said in September the system was out of touch with reality and that FIFA needed to set up an insurance policy.
"For releasing Arjen Robben, I heard we will get something like 57,000 euros from this $40 million pot but it (his salary) costs many, many times more," said Rummenigge.
"The world of the top clubs is maybe different to what they think."
Nearly $2 million was handed out to clubs from Japan, whose national side were knocked out in the second round, while clubs from Ghana, who reached the quarter-finals, received only $222,000 between them.
Clubs from semi-finalists Uruguay, who had only two home-based players in their squad, received only $186,000.
FIFA said that a total of 400 clubs from 55 countries received payments.
