Adilabad sessions court also dismissed the bail plea of Azeem-bin-Yahya, a co-accused in the case.
Opposing the bail plea of MIM leader, Additional Public Prosecutor B Praveen said the investigation was not yet complete, and the accused was involved in several other cases.
Mr Owaisi's counsel had said earlier that his client was ready to submit the passport to the court if there were any apprehensions about his movement upon release.
Mr Owaisi and Azeem-bin-Yahya are under judicial remand till February 5, lodged at Adilabad District Jail.
Police arrested Mr Owaisi, leader of MIM in Andhra Pradesh Assembly, on January 8 in connection with a speech made by him in the district, targeting a community, last year.
In a related development, the Nizamabad district police today took custody of Mr Owaisi from Adilabad District Jail and produced him at the residence of Second Additional Magistrate who remanded him in judicial custody till February 7 in connection with the hate speech case registered by Nizamabad Two Town police.
He was later taken back to Adilabad District Jail.
Apart from Nirmal police station case in Adilabad and the Nizambad case, Mr Owaisi is facing cases in Hyderabad, Kadapa and Karimnagar districts.