Police took action after Mr Zelaya's supporters defied a curfew
Honduran security forces have broken up protests outside the Brazilian embassy in Tegucigalpa in support of deposed President Manuel Zelaya, reports say.
Police have surrounded the embassy, where Mr Zelaya is staying, and the scene is now said to be calm.
Brazil's President Luiz Inacio Lula da Silva urged Mr Zelaya not to provoke a confrontation, AP news agency reports.
Mr Zelaya made a surprise return on Monday after months of exile. Interim authorities say he must face trial.
But the US and other governments have joined Mr Zelaya in calling for a negotiated settlement to the crisis, which began when Mr Zelaya was forced out of the country at gunpoint on 28 June.
Security forces surrounded the embassy and used tear gas to disperse thousands of Mr Zelaya's supporters in an operation that began in the early morning local time on Tuesday.
Gary Duffy, BBC News, Sao Paulo
The Brazilian authorities recognise that their staff in Honduras are caught up in a very delicate situation.
The ambassador is back in Brazil, there is only a charge d'affaires and a very small team, with not much security. Lights, water and telephones were cut off yesterday and the only contact is by mobile phone.
However, President Lula has expressed his complete support for Mr Zelaya and the ministry of foreign affairs here says he will not be asked to leave nor will he be handed over to the Honduran authorities.
The clear message from Brazil is that there has to be a negotiated solution to this crisis.
A protest leader, Juan Barahona, alleged that police had used live rounds, but this was denied by the interim deputy foreign minister, Martha Lorena Alvarado.
The demonstrators had defied a curfew imposed after Mr Zelaya made his dramatic appearance in the Brazilian embassy on Monday.
The Brazilian president said he spoke to Mr Zelaya, telling him not to provide a pretext for interim authorities to invade his country's embassy, AP reported.
Mr Lula reiterated his support for a negotiated end to the stand-off, reports said.
But inside the embassy, Mr Zelaya told Venezuelan broadcaster Telesur that interim authorities were cutting off all supplies to the embassy.
"I think they are going to employ a strategy of asphyxiating the embassy by surrounding it, cutting off the food supply, asphyxiating the people inside in order to demonstrate their force and power, and to try and humiliate the people in here who are really trying to find a solution, for dialogue at a national level," he said.
TIMELINE: ZELAYA OUSTED
28 June: Zelaya forced out of country at gunpoint
5 July: A dramatic bid by Zelaya to return home by plane fails after the runway at Tegucigalpa airport is blocked
25-26 July: Zelaya briefly crosses into the country at the land border with Nicaragua on two consecutive days, in a symbolic move to demand he be allowed to return
21 Sept: Zelaya appears in the Brazilian embassy in Tegulcigalpa
In an interview with BBC Mundo Ms Alvarado, the interim deputy foreign minister, said the government expected "that in the next few hours Brazil would either hand him [Zelaya] over or grant him political asylum".
Despite the international condemnation of the circumstances of Mr Zelaya's removal from office, she said, "that does not permit any embassy to use its diplomatic territory... to urge a civil uprising".
"It is fine that they support Zelaya's return but by force is not the way to proceed," she said.
"When Mr Zelaya was sent into exile, it was precisely to avoid what you are seeing now, disturbances directed by him," Ms Alvarado told BBC Mundo.
In addition to the curfew, airports have been shut and roadblocks set up on highways leading into Tegucigalpa.
Calls for calm
Earlier, Brazil's Foreign Minister Celso Amorim warned that any threat to Mr Zelaya or the Brazilian embassy would be a grave breach of international law.
The European Union also called for calm following Mr Zelaya's dramatic return to the country.
In a statement, it called on Mr Zelaya and the interim government to negotiate an end to the three-month crisis.
It added its voice to that of US Secretary of State Hillary Clinton, who said Mr Zelaya's return must not lead to violence.
Are you in Honduras? What is your reaction to Manuel Zelaya's return? Did you witness the protests? Send your comments using the form below.
A selection of your comments may be published, displaying your name and location unless you state otherwise in the box below.
You can also send your pictures and video to email@example.com or text it to +44 7725 100 100. If you have a large file you can upload here.
At no time should you endanger yourself or others. Click here forterms and conditions.
The BBC may edit your comments and not all emails will be published. Your comments may be published on any BBC media worldwide.