He was forced from the presidential palace by Honduran troops on June 28, the same day that he planned to hold a referendum opposed by the courts, military and business leaders.
Avi Lewis, Al Jazeera's correspondent in Tegucigalpa, said that police also moved against demonstrators who had gathered outside a media station that had been closed down on Monday, hours after the decree restricting civil liberties was imposed.
|Zelaya has stayed at the Brazilian embassy in Tegucigalpa since his return home [AFP]
"People gathered here in the streets today; more than 1,000 people. It was the largest demonstration in many days ... A huge crowd of police officers arrived. They put on their gas masks and were ready to disperse the crowd," Lewis said.
"The protesters agreed that they would let cars through - the police said that they would let them stay for an hour, and then the demonstrators would have to disperse.
"When the police later turned up to say they had to leave, the protesters started to leave. Then, all of a sudden, the police began to chase them. They fired tear gas at the fleeing demonstrators."
The military-backed interim government, which is led by Roberto Micheletti, has also threatened to shut down the Brazilian embassy if Brazil does not meet a 10-day deadline to hand over Zelaya or grant him asylum.
"Anything can happen at the moment. It is a dictatorial regime," Rafael Alegria, a farm leader, said as the arrests at the agrarian institute went ahead.
"I've never seen anything like this in all of Honduras. They [the interim government] can do anything they like."
The arrests come in spite of a promise by Micheletti on Tuesday that the restrictions on civil liberties that he had ordered – and which had been criticised by some of his political allies - would soon be halted.
Zelaya on Tuesday urged his supporters "to demand that the closed media outlets go back on air", while Ban Ki-moon, the UN secretary-general, has called the threats to close the Brazilian embassy "unacceptable".
Oscar Arias, the Costa Rican president who was the mediator in a failed round of negotiations between Micheletti and Zelaya, on Tuesday urged the international community to help the elections scheduled for November take place.
Zelaya was forced from the presidential palace and into exile on the same day that he planned to hold a non-binding referendum on the constitution.
Opposition politicians, the supreme court and the military accused Zelaya of trying to win support for an extension to his single term as president.
Zelaya denied those claims, saying that the public vote was aimed at constitutional reforms necessary to improve the lives of the poor.