The official, Father Federico Lombardi, said that many of the events had led to people thinking deeply about topics such as inter-faith dialogue, anti-Semitism and Aids prevention.
The pope has aroused controversy on several issues. His quoted remarks about Islam being "evil and inhuman" prompted violent protests around the world.
Then, Catholic-Jewish relations were severely tested when he lifted the excommunication of Richard Willamson, a priest who was a Holocaust denier.
Bendict also angered health campaigners, politicians and activists by claiming that condoms aggravated Aids.
The incidents meant the pope's ability and judgment was questioned as never before.
Despite the episodes generating unprecedented hostility towards the Vatican, Lombardi said he was "convinced" the question of Christian-Muslim relations had been addressed more frankly following the pope's 2006 lecture at the University of Regensburg, in Germany, when he talked about Islam.
He also said that the "clamorous response" to Williamson's declarations had allowed the Vatican to reinforce its position on anti-Semitism, and that the pope's remarks on condoms had led to a "greater understanding" of "truly effective" HIV/Aids prevention strategies in Africa.
"Once the first wave of criticism had passed, people were able to do some real hard thinking, and they did. The subsequent reflections were serious, penetrating and well argued. It took a while for word of them to reach the public, but eventually the public did hear about and really benefit from these contributions to the discussion," Lombardi said.
The communciations head has come under fire himself for mishandling incidents or bungling their execution, and attacks have arisen from within and outside the Catholic church.
Last week he claimed the pope had never been a member of the Hitler Youth organisation, even though Benedict had declared his membership in the 1997 book Salt of the Earth.
Lombardi was also accused of backtracking on Benedict's rejection of condoms by allowing the remarks to be edited in a way that contradicted news reports.
He told the audience: "I am not saying everything we have done and are doing is perfect. We would be deluding ourselves if we thought that communication can always be controlled or conducted smoothly. Is there any great institution or personality that, finding itself constantly in the limelight, is not the object of frequent criticism? Why ought we to think that the pope ought to be an exception?"
Much of the pope's unpopularity with the secular world had been due to his refusal to compromise on key issues and not because the Roman Catholic church was "outmoded or out of touch" with the times, Lombardi added.
He said Benedict had the courage to "be himself" and "not become enslaved to the desire for approval", which was one of the "greatest idols of the modern world".
No responsibility or liability shall attach itself to us or to the blogspot ‘Clerical Whispers’ for any or all of the articles placed here.
The placing of an article hereupon does not necessarily imply that we agree or accept the contents of the article as being necessarily factual in theology, dogma or otherwise.