"When I arrived at Harare airport I was not met by officials from the ministry of foreign affairs as before, but by immigration officials who told me that there was no clearance for my entry into the country," Nowak told Al Jazeera by telephone late on Wednesday.
"They confiscated my passport, of course ... and now they have brought me to the departure part of the airport where I am sitting in the lounge."
Nowak was told in Johannesburg that his visited had been postponed due to talks between mediators from the 15-nation South African Development Community (Sadc) and leaders of the power-sharing government, the UN said.
"This is not the way the United Nations should be treated"
UN special rapporteur
The mediators are hoping to resolve a standoff in the government between Tsvangirai's Movement for Democratic Change and the Zanu-PF party of Mugabe.
Tsvangirai temporarily withdrew from the power-sharing cabinet earlier this month accusing Zanu-PF supporters of human rights violations.
Opposition supporters and human rights defenders have accused Mugabe loyalists of violence, harassment and carrying out arbitrary arrests.
Nowak told Al Jazeera that he did not want to cancel the mission because he was responding to an official government invitation and the team he was travelling with had already spent a lot of UN money on the trip.
"First of all when I started the mission, upon arrival for transit in Johannesburg, they toldd they wanted to stop me. I did postpone actually for one day ... but the prime minister of this country wants to meet me tomorrow [Thursday] at 10 o'clock in the morning," he said.
"This is not the way the United Nations should be treated."
The invitation marked the first time that Zimbabwe had offered to open up to an expert working for the UN human rights council.