A ministry statement said members of a "terrorist cell" were killed in a fierce gunbattle, and five were captured, but did not say whether the pilot, Oscar Perez, was among the dead or detained.
At the height of street protests against President Nicolas Maduro last June, Perez and unidentified accomplices flew over Caracas in a police helicopter and dropped four grenades on the Supreme Court before opening fire on the interior ministry. There were no casualties.
Perez has been on the run since Venezuelan authorities issued an arrest warrant through Interpol after accusing him of a "terrorist attack."
The 36-year-old former elite police officer and actor has regularly taunted the government during his time in hiding, saying he was fighting against Maduro's "tyranny" and the "narco-dictatorship."
He urged Venezuelans "not to lose heart. Fight, take to the streets, it is time we are free."
Two weeks after the attack on the Supreme Court, Perez -- at the time Venezuela's most-wanted man -- turned up at a Caracas ceremony to commemorate those who had died in the wave of anti-government protests.
In all, 125 people were killed between April and July as authorities used force to put down protests to unseat Maduro.
Eventually, the protests fizzled out and the socialist president prevailed, despite a staggering crisis caused by falling oil prices, spiraling inflation and corruption.
"These terrorists, who were heavily armed with high-caliber weapons, opened fire on the officials responsible for their capture," the interior ministry statement said.
It said those who resisted had been killed.
The police were "attacked violently" when they were negotiating the surrender of Perez's group, it said, adding that they had "tried to detonate a vehicle loaded with explosives."
AFP journalists trying to reach the area saw an army tank, special forces and ambulances rush to the scene.
"They are firing at us with grenade launchers. We said we are going to surrender but they do not want to let us surrender. They want to kill us," a bloodied Perez said in one of several dramatic videos posted online.
Perez, a former elite police officer, is seen with other men in one of the videos, some of them armed.
He said they were being besieged by snipers.
"We will die standing up defending our land, never kneeling before the tyrants," another of Perez's messages said.
Vice president of the ruling Socialist party, Diosdado Cabello, said on Twitter the Police Special Action Force (FAES) had launched the operation to arrest Perez.
He said the security forces had "responded with fire" when two officers were wounded in the operation.
Iris Varela, Venezuela's minister with responsibility for prisons, rejoiced at the news that police had finally cornered Perez "like a rat."
"What a coward now that he has been caught like a rat. Where is the courage he had to attack military units, kill and injure officers and steal weapons?" she wrote on Twitter.
In December, Perez claimed responsibility for an attack on a military base in the country's north, in which weapons were seized.
Perez said in a message to his children that his fight against the government was dedicated to them and to the children of Venezuela, suffering the worst of the food and medicine shortages caused by the economic crisis.
Perez, blond and blue-eyed, was well known to Venezuelans even before his attack on the Supreme Court -- as an actor. He starred in the film "Muerte Suspendida" (Suspended Death), an action movie based on the true story of the kidnapping of a Portuguese businessman in Caracas.
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