The interior ministry said it killed four militants during Saturday'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."
Both sources declined to be named.
Asked about the claims, the interior ministry said that police in the Eastern Province, which includes Awamiya, were to issue a statement.
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On Saturday, 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 Saturday'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.
The town, just west of Dammam city on the Gulf coast, has witnessed clashes between security forces of the Sunni dominated kingdom and protesters from the minority Shiite community.
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.