Zelaya's attack on the congress came a day after the congress voted to hold an investigation into his mental state.
"Congress cannot investigate me, much less remove me or stage a technical coup against me because I am honest, I'm a free president and nobody scares me," Zelaya told congress.
"You have declared war against me. Now face the consequences."
Shops and petrol stations were closed on Friday in the capital, Tegucigalpa, after the city's chamber of commerce called on its members to shut amid fears of street violence.
Thousands of Zelaya's supporters had accompanied the president to Honduras' main airport earlier in the day, where they seized referendum ballots to stop them being confiscated by order of the courts.
Zelaya, who leads the Liberal Party, has said that the constitution does not give enough power to Honduras' poor and that the political elite is benefitting unfairly from the current charter. About 70 per cent of Hondurans live in poverty.
The president's supporters say that a coup d'etat is a prospect.
Military chief sacked
Zelaya sacked General Romeo Vasquez, the head of the Joint Chiefs of Staff, earlier this week after the military chief said he would not support the referendum.
The country's defence minister and the chiefs of the army, navy and air force have resigned in protest at Zelaya's bid to hold the vote.
"You have declared war against me.
Now face the consequences"
president of Honduras
But the president has the support of labour leaders, farmers and civic organisations, who say that the changes to the constitution are needed to improve the lives of the majority.
Zelaya has not said what changes he hopes to make to the constitution, but his opponents say that he is trying to rewrite the document to allow him to stand for re-election.
Zelaya is due to stand down from the presidency at the end of a four-year term in January.
The congress, the supreme court and the country's attorney general say that clauses in the constitution preclude certain changes being made to it, and that a referendum is therefore illegal.
PJ Crowley, a spokesman for the US State Department, said: "We are concerned about the breakdown in the political dialogue among Honduran politicians over the proposed June 28 poll on constitutional reform.
"We urge all sides to seek a consensual democratic resolution in the current impasse that adheres to the Honduran constitution and to Honduran laws, consistent with the principles of the Inter-American Democratic Charter," he said.
Crowley called on the Organisation of American States (OAS) to "take all appropriate actions" to uphold the constitution.
Larry Birns, the director of the council on hemispheric affairs, told Al Jazeera: "The US is making up with [Venezuelan President Hugo] Chavez and scheduling negtiations with [President Raul] Castro in Cuba.
"I don't think that the US would sacrifice these new beginnings for doing CIA hanky-panky stuff with the Honduran military.
"I think the US military will keep out of this ... for the time being."