The witnesses said in an audio testimony sent to Reuters by a local activist that an explosion was followed by shooting in Imam Rida Mosque in the town of Mahasen in the al-Ahsa region of the oil-producing province.
"The explosion happened outside the mosque, at the courtyard of the mosque, while another one entered with a machinegun. There are martyrs and wounded," the witness said.
"The young men grabbed his gun and beat him up, but he did not die. The police then came and took him away and the wounded were taken in private cars because ambulance cars did not arrive quickly."
Videos and photos circulated on social media showed at least three people lying apparently motionless inside the mosque, one with a mutilated hand. A separate video footage showed police firing in the air trying to disperse an angry crowd as they held one suspect in custody. There was no immediate claim of responsibility for the attack.
Sunni Muslim-ruled Saudi Arabia, the world's top oil exporter, has suffered a spate of deadly shooting and bomb attacks in recent months, many of them claimed by Islamic State militants.
Islamic State is bitterly opposed to Gulf Arab rulers and is seen as trying to stir up sectarian confrontation within Arabian peninsula states - Shias are a restive minority in Saudi Arabia - to bring about the overthrow of their dynasties.
Saudi-owned al-Arabiya television channel also reported that three people were killed in the mosque attack in al-Ahsa and that one suspect was arrested by the authorities.