In the 2010 event in the House of Commons, Israel's actions were compared with the Nazis.
The Labor leader, who has long fought anti-Semitism within his party, said he regrets appearing before people whose views "completely reject".
"Critics within the Labor Party have said that it went beyond normal decency."
His apology comes after a member of the ruling National Executive Committee of the Labor Party said that Jews "Trump fanatics" were behind the accusations of anti-Semitism.
In the 2010 event in the Commons, the Jewish survivor of Auschwitz and the anti-Zionist Hajo Meyer gave a talk entitled The misuse of the Holocaust for political purposes.
Meyer, who died in 2014 at the age of 90, compared Israeli politics with the Nazi regime.
The Times said that Palestinian activist Haidar Eid also addressed the meeting and said: "The world was absolutely wrong to think that Nazism was defeated in 1945.
"Nazism has won because it has finally managed to Nazify the conscience of its own victims."
Veteran Jeremy Corbyn critic John Woodcock resigned in July 2018
Mr. Corbyn has said: "In the past, in the search for justice for the Palestinian people and peace in Israel / Palestine, I sometimes appeared on platforms with people whose opinions I completely reject.
"I apologize for the worries and anxiety this has caused."
Backbench Labor MP John Mann He said it was "extraordinary" that the Labor leader had held a "protest event" on Holocaust Remembrance Day in 2010.
The long-time critic of Mr Corbyn he told the BBC Radio 4 Today program: "It violates any form of normal decency."
Karen Pollock MBE, executive director of the Holocaust Educational Trust said: "On Holocaust Memorial Day, when people from all backgrounds, festivals and religions gathered to remember the unique evil of the Holocaust, Mr. Corbyn chose to preside over an event that it undermines its purpose – deliberately distorting the truth of the greatest crime in history. "