"Let us be frank," the secretary general declared. "We have not yet achieved the sweeping and fundamental reform I and many others believe is required."
On the decision to drop all references in the final text to disarmament, he added: "We have allowed posturing to get in the way of results. This is inexcusable. Weapons of mass destruction pose a grave danger to us all."
Mr Annan and several other leaders, including President George Bush and Prime Minister Tony Blair, nonetheless used their appearances at the three-day summit to emphasise those areas where progress has been made. When they leave here, the 191 members of the UN will have committed themselves to a number of new initiatives, though many of the operational details involved are yet to be worked out.
These will include agreement in principle on replacing the Human Rights Commission in Geneva with a new and smaller body called the Human Rights Council as well as the creation of a new Peace-Building Commission to help countries emerge from armed conflict. For the first time world leaders will also pledge to intervene in countries where populations are threatened by massacre and genocide.
The genocide passage was welcomed by aid agencies such as Oxfam, which have otherwise expressed frustration with the scaling back of the summit's ambitions, particularly on development. "We must find time to celebrate one historic achievement," said Nicola Reindorp, the New York representative of Oxfam.
But there was little disguising the bruises left by the frantic negotiations in the days and hours leading up to the summit which led to so much being dropped or diluted in the blueprint for reform and action on development and disarmament originally tabled by Mr Annan. Most infuriating for many Western nations, Britain included, was the muddled language that emerged on combating terrorism.
Mr Bush and Mr Blair led the UN Security Council yesterday in adopting a UN resolution on committing countries to hunt down those who incite terrorist acts and foment terror-styled ideologies in schools and cultural institutions.
In a speech that was notably upbeat in offering support to the United Nations - a body whose standing in Washington has arguably reached a historic low - Mr Bush pressed other leaders to "put terrorists on notice" by cracking down on any activities that could incite deadly attacks.
"The terrorists must know that wherever they go they cannot escape justice," Mr Bush told the other leaders. "We must send a clear message to the rulers of outlaw regimes that sponsor terror and pursue weapons of mass murder: You will not be allowed to threaten the peace and stability of the world."
Facing an audience that was silent throughout his address - either out of respect or scepticism - the President lingered on trade policy, arguing that aid and debt relief were not enough to lift nations out of poverty, which he considers vital to helping contain terrorism and fanatical ideologies. In a thinly veiled challenge to the European Union, he called for the ending of farm subsidies in developed nations.
"The United States is ready to eliminate tariffs, subsidies and other barriers to the free flow of goods and services as other nations do the same," he said. "By expanding trade we spread hope and opportunity to the corners of the world and we strike a blow against the terrorists who feed on anger and resentment."
News from Iraq, where the insurgency yesterday claimed more than 100 lives, and from the US Gulf Coast seeped all day into summit proceedings. Making no apologies for the US invasion, Mr Bush instead pleaded for support. "The UN and its member states must continue to stand by the Iraqi people as they continue their journey," he said. "It's an exciting opportunity for all of us in this chamber."
Some speakers allowed themselves a touch of schadenfreude meanwhile by citing Hurricane Katrina. Even Mr Annan could not completely resist the temptation, without mentioning the storm by name.
"Whether our challenge is peacemaking, nation-building, democratisation or responding to natural or man-made disasters, we have seen that even the strongest among us cannot succeed alone," he said.Reuse content