The contradiction suggested differences had emerged within his party over implementation of a September power-sharing pact that could add to uncertainty over whether a new Zimbabwean leadership would be united enough to tackle economic crisis.
The differences could deal a blow to the constitutional amendment, if renegades in the MDC decides to go against their leader.
World Health Organisation figures mapping the spread of cholera in the country underlined the urgency of the matter.
Regional leaders decided at the meeting on Tuesday that Zimbabwe should form a unity government next month. But the opposition Movement for Democratic Change issued a statement saying the outcome fell "far short of our expectations", raising doubts over chances of ending the political deadlock.
Mugabe, who has made it clear he would set up a government without the opposition if need be, said talks were concluded and a new cabinet could now be formed.
South Africa’s Star newspaper quoted Tsvangirai as saying that resolving outstanding issues over a government was a "work in progress".
"Everyone agrees that — subject to the clearing of all the issues that are outstanding — a coalition government can be formed," he said.
"After all, the whole idea of these negotiations is to form a coalition government, and I therefore agreed to that principle."
The 15-nation Southern African Development Community (SADC) said after a summit in South Africa — its fifth attempt to secure a deal on forming a unity government — it had agreed that Tsvangirai should be sworn in as prime minister by February 11.
But the MDC quickly issued a statement after the SADC communique, making clear its disappointment and raising the possibility that deadlock would drag on.
The MDC said its national council would meet to define its position on the summit.
The signing of the pact was seen as a chance to prevent a total economic collapse that would add to the strain on neighbours already hosting millions of Zimbabweans who fled in search of work.
Others are escaping a cholera epidemic that has pressured rival parties to form a government and tackle the humanitarian crisis.
A cholera outbreak has killed over 3,000 people and infected more than 57,000 Zimbabweans, the World Health Organisation said on Wednesday.
WHO figures showed an increase of 57 deaths and 1,579 new infections since Tuesday. The outbreak is the biggest and deadliest in Africa in 14 years and underlines the need for a clarity within the MDC abd a settlement with Mugabe.
Zimbabwe’s state-run Herald newspaper said MDC Secretary-General Tendai Biti had made a "sudden U-turn" over implementing the deal.
"There are struggles going on internally, between the pragmatists and the hawks in terms of their contrasting positions on the power-sharing arrangement," said Zimbabwean political analyst Eldred Masunungure.
"This presents a test for Tsvangirai, but I have no doubt that he will prevail over any internal opposition to his decision."