It follows an EU ministerial meeting on Wednesday under the title, 'The heritage in 21st century Europe of the crimes committed by communist regimes'.
The meeting in Tallinn was organised by Estonia, which is the current holder of the rotating EU Council presidency.
The event was timed to coincide with the Europe-wide Day of Remembrance for the victims of totalitarian and authoritarian regimes.
Some MEPs, however, have branded the meeting as a "whitewash" and an "insult to European historic memory."
GUE/NGL group MEPs asked EU justice ministers, "especially those of progressive orientation", to boycott the event.
However, the only member state known to be absent was the Greek government.
Parliament's left-leaning GUE/NGL group said the event was "historically and politically biased" and "unacceptable under EU norms."
A statement issued by the group read, "We strongly condemn the organisation by the Estonian presidency of this ministerial meeting."
It went on, "At a time when the far-right and neo-Nazis are taking advantage of the failures of EU policies, equating nazism with communism is historically false, dangerous and unacceptable.
"Moreover, the fact that the Estonian government chose to focus on 'communist crimes' clearly shows an intent to use the institution of the rotating EU presidency for ideological purposes.
"This type of event undermines political dialogue and coexistence in Europe and is an insult to the historic memory of the European people."
Meanwhile, Commission First Vice-President Frans Timmermans said the Day of Remembrance on 23 August was for the victims of "all totalitarian and authoritarian regimes."
The Dutch official said, "We remember the victims of these regimes and we restate our rejection of the ideologies they were built on.
"Totalitarian regimes across Europe restricted people's freedoms; violated their rights and made millions of ordinary citizens victims of their ideology. We must remember past horrors to give us the knowledge and strength to reject those who seek to revive these ideologies."
Timmermans added, "The EU was built on the common values of human dignity, fundamental rights, rule of law and democracy, and on the rejection of extreme nationalism. We must never take these rights and freedoms for granted. We pledge to fight for them every day.
"Extremism, nationalism, xenophobia and hatred can still be heard in public speech in Europe. Keeping these memories alive is not only a tribute to the victims but also a way to ensure that these ideologies can be forcefully rejected and such atrocities never happen again."