Mbeki is mediating the talks at a secret location near Pretoria, the South African capital.
"There are naturally some matters which require the negotiators to come back to consult. That's why they are all here in Harare today," he said.
Mbeki said he had already met Morgan Tsvangirai, the leader of the MDC in Pretoria on Tuesday after the negotiations had adjourned.
In Harare, he also met Arthur Mutambara, the leader of another MDC faction.
"Yes there is progress and we remain committed to a settlement to the Zimbabwean crisis," Mutambara told AFP news agency
Earlier, the 84-year-old Mugabe expressed his "total commitment" to the negotiations, insisting they were "going well".
Tsvangirai, Mugabe and Mutambara signed an accord on July 21 to begin talks on sharing power after a months-long election dispute.
While Tsvangirai believes his victory in the first round of a presidential election in March should give him the right to a greater share of power, sources inside the MDC say Mugabe's negotiators are only offering him the chance to become one of several vice-presidents.
The former trade union leader has twice been charged with treason and needed hospital treatment for head injuries last year as he was assaulted by members of the security forces ahead of an anti-government rally.
The MDC said in a statement on Wednesday that two more of its activists were killed last week, allegedly by Zanu-PF supporters.
"The deaths show that there is no sincerity on the part of Zanu-PF. The death of the two brings to 122 the number of MDC activists who have been murdered since the March 29 harmonised elections," the statement said.
Mugabe and Tsvangirai are under pressure from within Africa and the rest of the world to negotiate a national unity government to end a crisis that has ruined Zimbabwe's economy and flooded neighbouring states with millions of refugees.