It's not just activists who are complaining about the crackdown. Business owners are saying the rules are unfair, and they're pointing to the low levels of registration as evidence.
In fact, up until two hours before the window expired, businesses had only submitted applications for 23 percent of the 600,000 eligible immigrants.
Although employers had been given close to five months' notice for the E-Card deadline, the blame for this paltry registration may not entirely lie with employers.
"A lot of SMEs (small- and medium-sized enterprises) paid the agents, but were never able to get E-Cards or the rehiring done," Kang Hua Keong, national president of the SME Association of Malaysia, reportedly told Channel NewsAsia. "A lot of agents promised — even blacklisted ones — that they can get it done, but actually, it is not true. Agents just want to make the money.''
Employers also faced risks in registering for the card, which could explain why many did not go through the process, according to Paul.
"Not everyone who applies can get the card," he said. "If you apply for the card, and your worker is found to not be eligible for it, he or she will be sent back."
Furthermore, although the E-Card is free, employers must pay 600 Malaysian ringgit ($140) in advance to legally rehire their worker at the end of the amnesty period. There is no refund if the application fails.
Nonetheless, others in Malaysia's business community held a different view.
"Admittedly, the government has given plenty of time for employers to comply with E-card registration," said Foo. "However, the employers take a wait and see attitude, thinking that government will extend the time for E-card application."
E-Card holders who do not obtain the necessary documents from their embassies for securing a Malaysian work permit by February 15, 2018 face deportation.