A UN official privately called it a "show camp", our correspondent says.
But Mr Ban denied his visit was being used by the junta to give a misleading picture of the crisis in Burma - also called Myanmar.
The issue of aid "should not be politicised", he said. "Our focus now is on saving lives."
Before embarking on the tour, he told reporters: "I praise the will, resilience and the courage of the people of Myanmar. I bring a message of hope."
'Drinking from puddles'
Earlier, in a meeting with Prime Minister Thein Sein, Mr Ban stressed international aid experts should be rushed in, according to the UN official at the talks.
"The United Nations and all the international community stand ready to help to overcome the tragedy," Mr Ban is quoted as saying.
But Burmese officials told Mr Ban in private meetings that the relief phase was ending and reconstruction would now begin.
Ban Ki-moon flew over southern Burma by helicopter to see the effects of the cyclone
Our correspondent says Mr Ban is concerned that aid is only reaching a quarter of those in need.
One foreign doctor told the BBC many were drinking water from puddles, while children and old people were suffering from dysentery, dengue fever and dehydration.
The generals have agreed that some UN helicopters can join the aid effort, but British, French and American naval vessels are still standing by off the Irrawaddy Delta, having been refused access to the area.
The first of 10 helicopters to be sent by the UN's World Food Programme arrived in Burma on Thursday, and will be used to ferry supplies to remote areas.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.