He said shots were fired during the incident, but that could not be independently confirmed.
“We have received reports that he was taken to a military air base,” Rafael Alegria, a senior government official, told pro-Zelaya television station Channel 8.
The president fired the armed forces chief of staff last week for refusing to help him organize an unofficial referendum Sunday on allowing presidents to serve more than a single four-year term.
The impoverished Central American country had been politically stable since the end of military rule in the early 1980s, but Zelaya’s push to change the constitution to allow him another term has split the country’s institutions.
The Supreme Court last week came out against Zelaya and ordered him to reinstate fired military chief General Romeo Vasquez — a move the president said amounted to a “coup” against him.
The pro-government TV channel Sunday called on Zelaya supporters to gather in the capital to support the president, but then went off the air without explanation. Phone calls to the presidential palace went unanswered.
The global economic crisis has curbed growth in Honduras, which lives off coffee and textile exports and remittances from Honduran workers abroad. Recent opinion polls have shown that public support for Zelaya has fallen as low as 30 percent.
Honduras, home to 7 million people, is a major drug trafficking transit point.
(Reporting by Mica Rosenberg and Gustavo Palencia; editing by Mohammad Zargham)