Several EU states have criticised Pope Benedict for saying that the use of condoms could endanger public health and increase the problem of HIV/Aids.
The Pope argued that distribution of condoms aggravated the problem, rather than helping to contain the virus, as he began a visit to Africa this week.
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.
The Roman Catholic Church believes marital fidelity and sexual abstinence are the best way to prevent the spread of HIV.
Some 22 million people are infected with HIV in sub-Saharan Africa, according to UN figures for 2007.
This amounts to about two-thirds of the global total.
French foreign ministry spokesman Eric Chevallier said: "While it is not up to us to pass judgment on Church doctrine, we consider that such comments are a threat to public health policies and the duty to protect human life."
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."
'Increasing the problem'
On his way to Cameroon, the Pope said HIV/Aids was "a tragedy that cannot be overcome by money alone, that cannot be overcome through the distribution of condoms, which can even increase the problem".
The solution lay, he said, in a "spiritual and human awakening" and "friendship for those who suffer".
Campaigners say condoms are one of the few methods proven to stop the spread of HIV.
Rebecca Hodes, of the Treatment Action Campaign in South Africa, said the Pope's "opposition to condoms conveys that religious dogma is more important to him than the lives of Africans".
On Wednesday, the Pope attended a gathering of more than 30 Cameroonian bishops in the capital, Yaounde.
He told the bishops they had to preserve traditional African families and protect the country's poor.
"In the context of globalisation with which we are all familiar, the Church takes a particular interest in those who are most deprived," he said.
He said it was the duty of Christians to help to build "a more just world where everyone can live with dignity", the Associated Press reported.
The Pope also warned of a threat to the Catholic Church in Cameroon from evangelical movements and from the "growing influence of superstitious forms of religion".
Earlier on Wednesday, he held a private meeting with Mr Biya at the presidential palace.
The BBC's Caroline Duffield in Yaounde says Mr Biya's consistent electoral victories have been widely condemned as fraudulent.
Having spoken out publically against corruption, many Cameroonians will be hoping that the Pope delivered his message in private as well, says our correspondent.
Pope Benedict is due to end his visit to Africa with a stop in Angola.