The head of a Malaysian conglomerate accused of running homes where hundreds of children and youths were allegedly sexually abused said there were 'one or two' cases of sodomy at the shelters but he denied other allegations of misconduct.

Police this week rescued 402 children from charity homes that authorities say were run by Global Ikhwan Services and Business (GISB) Holdings, an Islamic firm that the authorities have also accused of exploiting its workers.

Health screenings showed many of the children had injuries consistent with physical and sexual abuse, while 13 of them had been sodomised, police said on Friday.

GISB has said it did not run the homes and denied all allegations of abuse and exploitation of workers.

But in a video posted on GISB's official Facebook page on Saturday, Chief Executive Nasiruddin Ali said the company had broken some unspecified laws. "I don't want to blame the laws. It's true we have done some wrongs in the eyes of the law but couldn't there be some advice or discussions first?" he said.

Nasiruddin said allegations by police that children were sodomised and taught to sodomise others were "disgusting" but acknowledged there were cases of such abuses at the homes.

"Indeed, there were one or two cases of sodomy, but why lump them (the cases) all together?" he said.

GISB has been linked to Al-Arqam, a religious sect banned by the government in 1994. The firm has acknowledged the link but now describes itself as an Islamic conglomerate based on Muslim principles.

Malaysia's Islamic Development Department said in a statement on Saturday it would bring a report on suspected deviant teachings involving GISB to the cabinet, the national religious affairs council, and the conference of rulers. Malaysia has nine royal rulers who act as the custodians of Islam in the country.

Nasiruddin said some of GISB's accounts had been frozen and assets seized by authorities, adding that the firm was in the process of hiring lawyers to defend itself in court.

Following Wednesday's raids, police detained 159 people pending investigations and said its probe into GISB may be expanded to include financial offences.