Mkhize said the ANC were calling on "comrades to avoid using such solemn occasions to exacerbate tensions and embarrass the ANC".
Kathrada's memorial descended into chaos on Sunday afternoon as a rowdy crowd of ANCYL members heckled and booed speakers including Mkhize and former finance minister Pravin Gordhan .
This was despite the Durban High Court granting an interdict preventing members of the youth league from disrupting proceedings at the event held at Sastri College in Greyville, Durban.
Mkhize, who spoke last, was heckled with some league members saying that he had “sold out” by speaking publicly against President Jacob Zuma’s decision to reshuffle the cabinet.
"At a personal level such heckle does not affect me. I have been through worse situations and understand this in politics. For some people it's their way to express themselves," Mkhize said in a statement on Sunday.
"It is clear that the ANC leadership has a huge task to embark on political education to teach our youth tolerance of different views and respect for the memory of those who sacrificed their lives for our freedom, he said.
"The memorial service was a beautiful representation of the nonracial and non sexist credentials of the ANC from the youth to senior citizens many of whom have known struggle credentials.
"On behalf of the ANC we wish to apologise to those who were invited, for the embarrassment and inconvenience caused. The behaviour remains unacceptable now as it has always been when it happened to other leaders in the organisation as it erodes on the respect for the ANC.
"It is a challenge leadership has to address," he said.
Mkhize said: "There is need for leadership to dismantle factions which are tearing apart the organisation and urgently work to rebuild unity and deal with differences which play out in the open
"We call on all comrades to avoid using such solemn occasions to exacerbate tensions and embarrass the ANC."