Immigration director-general Datuk Seri Mustafar Ali personally led an enforcement team during a raid at a make-shift dormitory along Jalan Jati Kiri, Kapar just after midnight on Saturday.
Enforcement officers rounded up 239 workers and found 51 were without valid documents. They were later hauled away for further action.
The majority of the offenders were from Bangladesh.
Mustafar said most of the workers inspected were working for the nearby furniture and plastic manufacturing factories.
Surprisingly, the atmosphere at the dormitory was calm as the workers were grouped together during the inspection.
A female worker from Myanmar said she was not aware of the deadline.
"My boss went to get the cards but not everybody got them," she said, adding that her employer told them to not worry about it.
On Friday, Mustafar did not mince his words when he said that "there will be absolutely no extension" of the deadline for the E-Card registration.
"To those who thought we would extend the deadline, 'no way'. We have to show stern action. It might seem severe but we are protecting the country's interest and sovereignty.
"We will take action everyday to ensure this country is free of foreign workers working without permits," he added.
The deadline for the E-Card (enforcement card) registration ended on June 30.
Mustafar also said the department had conducted a comprehensive campaign to educate employers and foreign workers on the issue, including reaching out to the respective embassies.
The E-Card, which was launched on Feb 15, functions as a temporary confirmation of employment for illegal workers, which replaces valid travel documents from their respective countries.
The card is given out to employees for free, and is valid until Feb 15, 2018.
By Justin Zack