England rose two places after their Euro 2012 campaign with only Spain, Germany and Uruguay ahead of them - and are expected to achieve a highest-ever ranking of third next month.
Euro 2012 finalists Italy, who beat England in the quarter-finals, are sixth while Brazil have dropped from fifth to 11th - as 2014 World Cup hosts they do not play any competitive qualifiers so do not gain as many ranking points.
The rankings are important because they determine if teams will be seeded in the draw for the next World Cup.
Valcke told Press Association Sport: "I know that these rankings are sometimes quite difficult to understand due to the level and numbers of criteria that are taken into account.
"There are teams who are playing more friendly games than other teams and you can see a difference which is not very logical, but the ranking I would say 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 how this ranking is based."
FIFA's rankings are based on an international side's results over the previous four years, with more points awarded from competitive matches than qualifiers, and weighted even more strongly towards matches in the final tournaments of World Cups and continental tournaments such as European Championships.
England have benefited from the fact that their failure to qualify for Euro 2008 no longer counts against them when the rankings are calculated.