The official conceded that the approach, which was introduced at the end of 1992, can appear confusing, but stressed that the results are an accurate reflection of quality
England rose two places to fourth in the rankings, despite their quarter-final exit at Euro 2012, while vanquishers Italy, who finished second in the tournament, have moved up six places into sixth.
The Three Lions benefited from the fact that their failure to qualify for Euro 2008 is no longer considered, as the rankings are based on the teams' results from the last four years.
Brazil, on the other hand, have dropped six places into 11th, and it may not stop there. The Selecao will not take part in any competitive matches until the 2014 World Cup, held in their own country, because they do not have to qualify.
"I know that these rankings are sometimes quite difficult to understand due to the levels and numbers of criteria that are taken into account," Valcke told Press Association Sport.
"There are teams who are playing more friendly games than other teams and you can see a difference which is not very logical, but I would say the ranking is clearly still a good picture of the level of international football.
"Brazil are not playing official games, just friendly games as they are already qualified.
"There have been internal meetings and also with the football committee to discuss the ranking of the different nations. We want to be able to explain in an easier way on what this ranking is based."
Spain retained their place at the top of the list after winning the Euros, with Germany taking second place at the expense of Uruguay.