The President of Honduras was ousted in a military coup yesterday when troops arrested him in his pyjamas and sent him into exile in Costa Rica.

The military action against President Zelaya, the country’s most popular President in recent history, raised fears of widespread violence as supporters took to the streets, throwing stones at army lorries and shouting: “Traitors! Traitors!”

President Obama called for calm, saying that “existing tensions and disputes must be resolved peacefully”, and a State Department official said that Mr Zelaya was the only “elected and constitutional” leader of Honduras. The EU condemned the coup, while the Organisation of American States called an emergency meeting at its headquarters in Washington.

The UN Secretary-General, Ban Ki Moon, called for Mr Zelaya to be reinstated.

Venezuela’s leader threatened military action to abort the coup, the first in Central America since the end of the Cold War. President Chávez, who heads the Alba bloc of leftist Latin American countries, of which Honduras is a member, said that he had put his country’s troops on alert. “We will bring them down, we will bring them down, I tell you,” he said on state TV.

The military move came after Mr Zelaya vowed to push ahead with a controversial referendum that was due to take place yesterday, and refused to reinstate the military chief he had dismissed for opposing it.

The left-wing leader was seeking to change the constitution to allow him to stand for re-election — a path trodden by a string of regional allies such as President Chávez and President Morales of Bolivia. The military, the judiciary and even much of Mr Zelaya’s party were deeply critical of the planned vote, branding it illegal.

The Supreme Court said that it had ordered the removal of the President to defend the rule of law. The Honduran Congress later swore in its leader, Roberto Micheletti, as the new head of state after voting to remove Mr Zelaya for “manifest irregular conduct” and “putting in present danger the state of the law”. It had earlier accepted what it said was a letter of resignation from the President, though Mr Zelaya denied having written it.

Mr Zelaya was taken to an air force base outside the capital, Tegucigalpa, from where he was flown into exile to San José, the capital of Costa Rica. He spoke to a local television station later in the day. Mr Zelaya said that he was woken by gunshots and ducked behind an air-conditioning unit to avoid flying bullets while his security guards resisted troops for at least 20 minutes. He described the military action as both a “coup” and “kidnapping” and said that he still wanted to serve his full term, which ends in early 2010.

“A usurper government cannot be recognised by absolutely anybody,” Mr Zelaya said.

Shortly after the President’s arrest, soldiers in dozens of army lorries sped to the presidential palace and blocked the entrances and the hillside road leading to the seat of the Government. Tanks rolled through the streets as angry Zelaya supporters threw stones at them. Police fired teargas to disperse demonstrators while fighter jets screamed overhead.

The detention follows an escalating stand-off between Mr Zelaya and the military over the referendum plans. Hundreds of troops massed in the streets of the capital last week after the President dismissed the military chief, General Romeo Vásquez, ignoring a Supreme Court vote that he should remain in his post. As Mr Zelaya’s authority began to crumble, military commanders refused to distribute ballot boxes for yesterday’s vote. The Defence Minister, Edmundo Orellana, and the heads of the army, marines and air force all resigned.

Many Hondurans refused to accept the takeover as a fait accompli. “They kidnapped him like cowards,” Melissa Gaitán, 21, an employee of the official government television station, screamed, tears streaming down her face. “We have to rally the people to defend our President.”

Local media reports said that the airport was overwhelmed with foreign tourists desperate to find flights home. The fate of Britons in the country was unknown, with calls to the British consul in the capital and to the nearest embassy — in Guatemala City — going unanswered. The Foreign and Commonwealth Office said that it was monitoring the situation.

Mr Zelaya was elected as a conservative in 2006 but has since shifted across the political spectrum, aligning himself with the Latin American left-wing bloc led by Mr Chávez.

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