A bench headed by Justice Madan B Lokur perused the status report filed by the CBI and said "what is this going on? This is horrible".
The apex court also took note of allegations referred by the CBI against shelter home owner Brajesh Thakur and issued notice to him to explain why he should not be transferred to a jail outside the state.
The CBI in its report had alleged that Thakur is an influential person and a mobile phone was recovered from him inside the jail where he is currently lodged under judicial custody.
The bench also comprising Justices S Abdul Nazeer and Deepak Gupta noted that Thakur is an influential person.
The top court also asked the Bihar and CBI to explain delay in tracing whereabouts of ex-minister Manju Verma's husband Chandrashekhar Verma.
It had asked the Bihar Police to investigate the former minister and her husband in connection with the recovery of huge quantity of ammunition from them.
Verma had to resign as the minister of Social Welfare from the Bihar government in the wake of the Muzzafarapur shelter home sexual abuse case.
The bench said the CBI team investigating the case should not be changed and posted the matter for hearing on October 30.