France's foreign ministry said condoms were fundamental to prevention.
German ministers said it was irresponsible to withhold family planning from the poorest of the poor.
In Berlin, German Health Minister Ulla Schmidt and Development Minister Heidemarie Wieczorek-Zeul said in a joint statement: "Condoms save lives, in Europe as well as on other continents.
"Modern assistance to the developing world today must make access to family planning available to the poorest of the poor - especially the use of condoms.
"Anything else would be irresponsible."
Dutch Development Minister Bert Koenders said it was "extremely harmful and very serious" that the Pope was "forbidding people from protecting themselves".
"There is an enormous stigma surrounding the subject of Aids and Aids sufferers face serious discrimination," he added.
"The Pope is making matters worse."