In a sign that the interim government is under pressure over the raids, the de facto president said that the restrictions on civil liberties would soon be lifted.
Radio Globo has a reporter inside the Brazilian embassy in Tegucigalpa where Zelaya has been staying since he slipped back into the country a week ago in defiance of an arrest order against him.
Television station Cholusat Sur - viewed as critical of the interim government - was also raided early on Monday, Romero said.
Police and troops cordoned off the Radio Globo building and the offices of Cholusat Sur, witnesses said.
The stations were shut down a day after the government announced a media clampdown and a ban on unauthorised gatherings.
Both stations have been taken off air several times since the coup on June 28.
The new media restrictions, announced on Sunday, came as Zelaya called for a peaceful "final offensive" to mark the three-month anniversary of the coup which removed him from power.
Honduras authorities launch crackdown on media and civil liberties after Zelaya's return
Supporters of Zelaya gathered in Tegucigalpa, after the country's government threatened to close the Brazilian embassy for harbouring the ousted leader.
Mariana Sanchez, Al Jazeera's correspondent at the gathering in the capital, said: "Supporters here say they want to march to the embassy.
"A small group of riot police are here and they have the right to arrest these people, so there is a lot of tension here.
"These protesters are beginning to demonstrate in a much more visible way. They have said they will defy the law, they will defy the police authorities and will continue to gather."
Representatives of the Organisation of American States (OAS) held an extraordinary session on Monday to discuss the country's stand-off, a day after Honduras denied entry to an OAS delegation seeking to broker a solution to the crisis.
The US ambassador to the OAS criticised both the de facto Honduran leadership and Zelaya during the meeting in Washington.
"The regime should manage security with restraint and caution. President Zelaya should exercise leadership in urging his followers insistently with no mixed message to express their views peacefully," Lewis Anselem said.
He called the interim government's actions "deplorable and foolish" but also said that Zelaya ought to "desist from making wild allegations and from acting as though he were starring in an old movie."
Zelaya was forced from the presidential palace and into exile on June 28, 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.