He is said to have kicked the leader of COPE's youth wing, Anele Mda, out of the meeting following a stand-off.
According to party members who attended the meeting, Lekota rejected a request by provincial structures to seek political solutions to current infighting that continues to affect the organisation.
The insiders told The Times that Lekota and Mda argued for about two hours before the youth leader chose to abandon the heated meeting.
COPE has been plagued in recent months by leadership battles between Lekota and his deputy, Mbhazima Shilowa.
Last week, an initiative was formulated by the provinces to create a dialogue to resolve internal matters after the Cape Town High Court said the party leaders should work together.
The meeting was scheduled to take place on Saturday, but was postponed to yesterday as three provinces - KwaZulu-Natal, Free State, and Northern Cape - failed to attend.
A four-man task team was then set up to brief COPE's congress working committee.
Lekota apparently refused to listen to the team - Archie Ralo, John Ncebesha, and Neville Mompati - prompting Mda's insistence for him to give them an audience.
An official at the meeting said it was "ugly".
"Lekota would just not budge. He refused to listen to them and Anele took him to task," said the official.
"Though the meeting continued, issues remained unresolved.
"The point is the supposed leader of the party is refusing to engage in dialogue that would assist the party."
Lekota's spokesman, Phillip Dexter, said it was not Lekota alone who had kicked Mda out of the meeting, but the decision of the entire leadership.
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