It comes amid claims that supporters of President Robert Mugabe's Zanu-PF party have launched a campaign of violence.
MDC members say they have been beaten in recent days, despite the two parties being partners in a coalition.
Prime Minister Morgan Tsvangirai, MDC leader, withdrew co-operation with the unity government earlier this month.
He was angry at the jailing of a senior MDC member on terrorism charges that he says are trumped up.
Urgency 'highlighted'
The United Nations says Mr Nowak - the special rapporteur on torture - was informed of the cancellation only when he was in South Africa on his way to Zimbabwe.
He had been due to meet officials and rights activists and inspect prisons and police stations to compile a report for the Security Council.
The UN said Harare had called off the visit because of an unanticipated meeting with the southern African regional group, Sadc.
A Sadc team is due in Harare later to try to resolve the political crisis.
The UN said in a statement that Mr Nowak welcomed "all efforts to resolve the political crisis", but that the Sadc meeting was not a valid reason to cancel his visit.
"Recent allegations that MDC supporters and human rights defenders have been arrested, harassed and intimidated during the past few days, highlight the urgency of objective fact-finding by an independent UN expert," the UN said.
On Tuesday, Mr Tsvangirai's MDC party said there had been an increase in violent attacks on its members.
Party spokesman Nelson Chamisa said a senior official had been stopped and beaten by Zanu-PF supporters on Tuesday morning. Days earlier, an MDC residence was raided by police.
Zanu-PF has described the comments as "cheap propaganda".
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