Attorney-General Luisa Ortega told reporters that the arrest warrant was related to a May 2009 case in which Zuloaga was accused of illegally storing 24 vehicles.
In March, Zuloaga was arrested for statements he made in the Dutch island of Aruba, and charged with the crime of offending Chavez and spreading false information.
A Caracas court also ordered him not to leave the country.
|Chavez has accused Globovision of conspiring against him [Reuters]
The new arrest warrant came a week after Chavez publicly lamented that Zuloaga remained free.
"They caught that man with a bunch of cars in his house and that's a crime - hoarding. And he's free and he has a television channel," the Venezuelan leader said in a televised speech.
He called it a case of "structural weakness" in Venezuela's legal system.
Zuloaga, who also owns several car dealerships, has said he was storing the cars on his property for safekeeping because one of his dealerships had been robbed.
In a statement, the head of Venezuela's press association condemned the warrant as an attempt at political persecution.
"Once again it's been shown that in Venezuela there's no independence of powers, an essential value of democracy, since the judicial branch seems to act every time the president speaks or orders it," Alejandro Aguirre said.
"It worries us that this is happening increasingly frequently."
Chavez has long accused Globovision and other opposition media outlets of conspiring against him.
The TV station has been the only anti-Chavez channel on the air since another opposition-aligned channel, RCTV, was forced off cable and satellite TV in January.
RCTV had been booted off the open airwaves in 2007.