One worker is understood to have been taken to hospital after the second evacuation due to high levels of atmospheric silica.
Site sources told the Enquirer that the alarm was raised when tunnel ventilation fans were mistakenly turned on for testing forcing clouds of dust onto the platforms packed with construction workers.
The incident happened on Tuesday during a tour of the job by Unite union officials and main contractor Costain Skanska joint venture management.
Workers were put back to work on Wednesday only to be forced to evacuate the site later that day when they were overcome by heavy dusts.
The union was carrying out independent air quality checks following a series of mystery deaths on the site.
The Enquirer revealed last week that four workers have died in their sleep at home this year.
The deaths have caused concern among the workforce who have previously flagged fears over dust levels on the job.
A site source said: “It’s getting ridiculous down there now.
“This cannot continue and none of us down here are convinced this is a safe working environment.
“We can’t believe the HSE aren’t all over this and checking themselves exactly what is going on here.”
Both Crossrail and the joint venture contractors are preparing statements.