Barroso's comments appeared a day after Spanish media quoted Jose Maria Aznar, the former Spanish prime minister, as saying that Benedict had no need to apologise.
"Attacking the pope because he refers in a discourse to a historical document is completely unacceptable," Barroso said in a newspaper interview on Sunday.
He was referring to Muslim outrage at a lecture by the pope in his native Germany earlier this month in which the pontiff quoted a Byzantine emperor's criticism of Islam.
Asked why European leaders had not stood up to defend the pope's right to free speech, Barroso said: "Perhaps it is because there are concerns about a possible confrontation.
"I was disappointed that there were not more European leaders who said: 'Obviously the pope has the right to express his opinion.
"The problem is not the comments of the pope but the reactions of the extremists ... We must defend our values."
"Why do we always have to say sorry and they never do?" Aznar told a conference in the US on Friday, the Spanish media reported.
"It is interesting to note that while a lot of people in the world are asking the pope to apologise for his speech, I have never heard a Muslim say sorry for having conquered Spain and occupying it for eight centuries."
Aznar's government was voted
out after the Madrid attacks
This was a reference to the Muslim conquest of much of the Iberian Peninsula from the eighth to the 15th century.
Aznar, prime minister from 1996 to 2004, took the country into the US-led war in Iraq despite overwhelming public opposition. His government was voted out of office following Madrid attacks in March 2004.
"We are living in a time of war ... It's them or us. The West did not attack Islam, it was they who attacked us," he told the conference in Washington on "global threats".
"We must face up to an Islam that is ambitious, that is radical and that influences the Muslim world, a fundamentalist Islam that we must confront because we don't have any choice.
"We are constantly under attack and we must defend ourselves."