Authorities are investigating Global Ikhwan Services and Business (GISB) for allegedly running charity homes from which police last week rescued 392 children and youth. Police said many showed signs of sexual abuse and neglect.
The bank accounts held a total of more than 580,000 ringgit ($136,000) and the company is now being investigated for alleged money laundering as well as religious offences, the Inspector-General of Police Razarudin Husain told reporters.
"We are conducting our investigation transparently and fairly while protecting the rights of those concerned," Razarudin said.
GISB did not immediately respond to a request for comment.
The company had initially said it did not run the charity homes and denied all allegations of abuse, but then its chief executive said on Saturday GISB had broken unspecified laws and that there were 'one or two' cases of sodomy at the youth homes.
Razarudin said four of the 96 bank accounts that had been frozen were now shut, and that police had also seized 8 vehicles belonging to the company.
Authorities have said they would summon GISB's top management for questioning in the case, which has sparked outrage in Muslim-majority Malaysia and put the spotlight on the company's roots in a religious sect outlawed by the government three decades ago.
In a Facebook post on Tuesday, Malaysia's King Sultan Ibrahim, who acts as the custodian of Islam in the country, called for a thorough investigation into the case and for swift action to be taken against any wrongdoers.