FIFA said Beckenbauer, the task force's chairman, was suffering from health problems and England World Cup winner Charlton told the ruling body a week ago he would not be able to take part. Pele had a private commitment.
"It was unfortunate they could not be here but football was well represented," FIFA president Sepp Blatter told reporters.
"Pele is the king and the king has his own agenda.
Former Zambia forward Kalusha Bwalya, who chaired the meeting in Beckenbauer's absence, said the committee had agreed to propose allowing a fourth substitution during extra time.
"A lot was said about the way the players behaved at the last World Cup final but if you look at the team benches, one has to say this was not the best public relations exercise for discipline and respect," he said.
The 22-man group was formed as a response by FIFA to the drab, defensive football and controversial refereeing decisions which marred last year's World Cup in South Africa.
Former France international Christian Karembeu, Spain's Fernando Hierro and former Brazil captain Cafu are also part of the group.
It is due to produce a report for FIFA's annual Congress next year.
