Speaking in Parliament on Wednesday, Stavros Lambrinidis spoke about the importance of European values in promoting human rights around the world.
The Greek-born official told MEPs, "You have to recognise that we are not all the same."
His comments were challenged by several MEPs including Portuguese Socialist MEP Ana Gomes, who told the special representative that human rights violations within Europe itself had damaged the continent's credibility.
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Lambrinidis, himself a former MEP and Vice President of Parliament, was addressing the subcommittee on human rights on his work in the past 12 months.
He told the committee, "No one is perfect when it comes to human rights, including the west, but all the fundamental building blocks for human rights have been placed in increasing doubt. Many countries are sitting on the fence when it comes to human rights.
"The EU is right to strongly criticise human rights violations around the world and human rights violators, including those who are bent on violating human rights and are doing so in a massive way."
It was his reference to European values that angered some committee members, including Gomes, who said that in some parts of the world the EU and Europe were not seen as promoting human rights.
She said, "This is not the way Europe is seen in many parts of the world."
One example she cited was the perceived failure of the EU to have a human rights dimension in its migration and asylum policy.
Gomes said, "Europe is not seen so much as a continent which promotes 'values' and human rights but as a continent with guns and which possesses the brokers with these guns who are ready to use them. This is how we are seen and we need to understand that."
This, she said, was an example of the European double standards on human rights which had undermined its credibility in promoting such issues around the globe.
Gomes told Lambrinidis, "The EU discredits itself with such double standards and this does great damage to the otherwise very good work done on human rights issues."
She asked him, "Are we really serving security and good governance if we overlook human rights within Europe and also the links between human rights violations and corruption?"
Her comments were partly endorsed by another committee member, Marietje Schaake, a Dutch ALDE group MEP, who said, "We should not politicise European values because such values are universal."
She added that the EU and Europe was, in some cases, hypocritical on human rights issues, adding, "There is a risk of us losing credibility if we overlook human rights violations in Europe itself."
Schaake also said there had been an "erosion of human rights" around the world in the past year, adding that "human rights are too easily just thrown overboard in some countries."
In his response to their comments, Lambrinidis, a former Greek foreign affairs minister, told Gomes, "You said some strong things, some of which I do not agree with.
"Yes, there may be some countries in Europe that repress their people and the question of how we are perceived around the world is complicated. There is concern about how some member states do deal with human rights and how they apply human rights principles so it is legitimate to have a debate on this."
He told the committee that while human rights violations in Europe were not specifically part of his mandate he had raised such concerns with certain member states.
He added, "I have to say, however, that when it comes to human rights, many countries in the world still see the EU and Europe as a good example. They have seen how we have turned bloodshed on this continent into economic greatness."
In his formal presentation, Lambrinidis also noted the progress he says has been made in some countries on human rights.
"In Azerbaijan, by no means a country free of human rights violations, we have seen some good work with, for example, political prisoners being released.
"In Colombia, the peace deal is a remarkable turn of the page for human rights while with Iran, with have conducted the first human rights discussions in over a decade, with more to come later this year. The same has happened with Cuba."
On China, often criticised for rights violations, he said, "China wants to be seen as a world power but this is not just about the economy but also about respecting human rights and values and we shall continue to remind them of this."
Lambrinidis was criticised by some members for visiting some countries with bad human rights records, like Belarus.
He replied saying, "The easy thing for me would be not to go to some of these countries but sit in my office, say pious things and fire off press releases condemning this and that. But that would not make a difference."