Special police units searched house-to-house in the village of 1,600 inhabitants as snipers took up positions on the hills above and helicopters flew overhead.
Greek Police Chief Anastasios Dimoshakis traveled to Crete to coordinate the effort on the island, where gun ownership is widespread and police for decades have battled blood feuds as well as drug- and arms-smuggling by criminal gangs based in close-knit communities.
On Monday, about 20 gunmen wielding assault rifles had opened fire on the police convoy, wounding the three officers, one critically.
Dimoshakis on Tuesday called the incident unprecedented. "Greek police will assume their responsibilities. We have to ensure legitimacy," he said.
The raids follow the arrest last Friday of a 24-year-old in the Cretan town of Rethymno in possession of hashish and cocaine. His cousin, a suspected accomplice, escaped. The cousin's home in Zoniana is believed to have been the target of Monday's police raid.
Authorities have come under pointed criticism for allowing a climate of lawlessness to persist in parts of Crete, one of the country's busiest tourist spots.
Government spokesman Theodoros Roussopoulos on Tuesday said the strong police intervention was to stop drug gangs operating on the island and not out of revenge for the police attack.
"The police are not waging a war with anyone and have no open accounts with anyone," he said.
Interior Minister Prokopis Pavlopoulos said years of governmental inaction had allowed a climate of lawlessness in parts of Crete.
"There has been a lack of intervention by state and police authorities for years, (but) that is their responsibility," he said.
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