Mr Boutros-Ghali has simultaneously made it clear that he intends running as a candidate none the less, setting the stage for a potentially bruising struggle between governments sympathetic to him and the United States at a time when the UN is facing an array of delicate problems.
The former Egyptian foreign minister, who will be 74 in November, is well liked by most of the developing world. On the Security Council, at least China, Russia and France are believed to favour him for a second term. Britain yesterday refused to take any public position on his future.
The White House spokesman, Mike McCurry, indicated that the President had decided several weeks ago to block Mr Boutros-Ghali's re-election. Mr Clinton has come under intense domestic pressure to find a new candidate for the post, notably from Republicans on Capitol Hill. In the history of the UN, however, no previous Secretary-General has been denied a second term.
"The President now believes it is very important to get new leadership of a very vital international organisation that has many challenges," Mr McCurry said. "It is important to have leadership that is capable of reforming the UN bureaucracy and decreasing the cost of financing the United Nations."
The struggle to agree on a candidate for the post now begins in earnest and will culminate in an informal election, by a show of hands, inside the Security Council towards the end of this year. Because the US will be in a position to exercise a veto in the council, Mr Boutros-Ghali's prospects must be bleak indeed. Any change of heart by Washington seems unlikely.
Mr Boutros-Ghali, who is on an official visit to Germany, said yesterday: "I still hope that the US will change its position. We still have six months until the election." He is scheduled to visit London next Wednesday for talks with the Prime Minister, John Major, and the Foreign Secretary, Malcolm Rifkind.
In a non-committal statement, the Foreign Office praised Mr Boutros-Ghali as a "distinguished statesman who has served with honour in one of the world's most difficult assignments at a very testing period in the United Nations' history". Britain was not a supporter of Mr Boutros-Ghali when he was appointed in 1990 and is unlikely to oppose the US by supporting him now.
There was undisguised disgust from Mr Boutros-Ghali's inner circle in New York at the American decision.
"Because one member state says one thing, that should not necessarily be the rule of law. This is a democratic institution," said Ahmed Fawzi, a spokes-man for the Secretary-General. He suggested that Mr Boutros-Ghali had been undermined by an unfair campaign against him in the US media. "It is disheartening to see lies being said about this organisation. I am really sick of it." Mr Fawzi said the Secretary-General had been assured the support in his re-election effort from a "majority of the member states of the UN" and that this included specific pledges from "members of the Security Council".
For France, President Chirac has stated in recent weeks that he would like Mr Boutros-Ghali to serve another term. A spokesman of the French foreign ministry in Paris said yesterday: "There is a long tradition of secretaries-general being given a second term and you know the esteem and the regard in which we hold Mr Boutros-Ghali." The spokesman stopped short of pledging to fight the US on the issue, however.
Three figures who have been mentioned in recent weeks as possible replacements claimed yesterday that they would, in fact, not be running. They include the President of Ireland, Mary Robinson, the chief of the UN High Commission for Refugees, Japan's Sadako Ogata, and Gro Harlem Brundtland, the Prime Minister of Norway. The name of Kofi Annan, a Ghanaian who is the chief of UN peace-keeping, has also been mentioned.
Resentment is sure to boil up inside the United Nations at the position taken by the US. A large number of developing countries make little secret of their contempt for the role of the US in the organisation, especially since it owes it some $1.5bn (pounds 1bn) in unpaid dues, roughly half of the UN's debt.
For over-burdened, virtually bankrupt international organisation. Responsible for peace, happiness, health and prosperity on planet Earth. Must have friends in high places, including Washington, Paris and CNN. Five-year contract, with possibility of extension (but don't bet on it). Salary: $286,000 a year. Perks: well-appointed Manhattan townhouse, chauffeur- driven limousine, blue beret provided. Start 1 January 1997. Women candidates most welcome.
THE INCUMBENT AND THREE LADIES-IN-WAITING
Boutros Boutros-Ghali: Former Egyptian Foreign Minister appointed to top job in 1990. Popular in the developing world and favoured by China, Russia and france onm Security Council. But Clinton is under pressure to replace him and has now made intention clear
Mary Robinson: Elected 1990 as Ireland's first woman president, Robinson, 52, has been touted as a candidate by Irish-Americans. Has said she was not interested in UN post, but this month spoke of her views on the future of the organisation and her vision of globalisation.
Gro Harlem Brundtland: Became Norway's youngest Prime Minister in 1981, when she formed first of several governments, most recently in 1990. A former leader of Norway's Labour Party, Brundtland, 57, served as head of the UN Commission for the Environment and Sustainable Development.
Sadako Ogata: Former dean at Tokyo's Sophia University, Ogata, 68, was elected UN High Commissioner for Refugees in 1990 and is considered one of the organisation's most effective administrators. Her agency is one of the UN's largest, and cares for millions of refugees worldwide.