The interior ministry said it killed four militants during yesterday's operation in Awamiya town to arrest the suspects who shot dead a soldier a week earlier.
But residents gave the toll as five and said they included a youth aged 16 or 17.
"One of them I'm sure is not involved," an activist in the area said. "He was killed in his car."
A resident of Awamiya said the youth appeared to have been killed "by mistake. One of the bullets got in his neck, while he was driving."
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Asked about the claims, the interior ministry said that police in the Eastern Province, which includes Awamiya, were to issue a statement.
Yesterday, the ministry said the four militants died during a shootout. They included the prime suspect in the killing of soldier Abdelaziz bin Ahmed al-Assiri, who died on December 14 when security personnel came under fire from farms near Awamiya.
Photographs circulating on the Internet purported to show a building riddled with bullet holes from yesterday's operation, armoured cars in the streets, and burned civilian vehicles.
"It's actually a big operation" which left townsfolk cowering inside their homes, the first resident said, adding that some of those killed were well-known as "criminals" in the area.
Earlier this month, a court sentenced to death a man who opened fire numerous times on police in Awamiya.
Most Saudi Shiites live in the oil-rich east, and many complain of marginalisation.