The MDC offered a different take on events, saying: "The MDC ministers held a meeting at the party headquarters while Zanu-PF ministers held a Zanu-PF minister caucus meeting elsewhere."
'Dishonest and unreliable'
Tsvangirai gave warning last week that the MDC would disengage from Mugabe's "dishonest and unreliable" Zanu-PF party in the unity cabinet.
The boycott has created the country's most serious political crisis since the formation of the new administration in February.
Tsvangirai has headed to Mozambique to appeal for regional help in his standoff with Mugabe.
"The president is going to meet with the prime minister of Zimbabwe today," Marlene Magaia, Guebuza's spokeswoman, said on Tuesday.
"It has to do with the current situation in Zimbabwe."
Tsvangirai was in the South African city of Johannesburg on Monday and plans to also meet Joseph Kabila, the president of the Democratic Republic of Congo and chairman of SADC, as well as Jose Eduardo dos Santos, Angola's president.
The MDC said that Tsvangirai would be "explaining the MDC's decision to disengage".
Tsvangirai has said he has not quit the government but will only resume unity relations once unresolved issues - including disputes over key posts and a crackdown against his supporters - are settled.
Political tensions in Zimbabwe have also been heightened by the renewed detention of Roy Bennett, a white aide to Tsvangirai, on "terrorism" charges.
Bennett is is due to go on trial on November 9.
After years of economic free fall under Mugabe's sole rule, Zimbabwe has seen an easing of international ties and rebuilding of shattered infrastructure and social services.
But donors say they want more reforms before increasing aid.