Mr Owaisi's medical report shows he has a hernia, adhesions in his abdomen, and is finding it difficult to walk on account of complications from a bullet injury in his right thigh.
Sources say that based on doctors' advice, the police decided to arrest him.
The legislator who belongs to the Majlis-e-Ittehadul Muslimeen or MIM party in Andhra Pradesh, was escorted by an ambulance and heavy security to the Gandhi Hospital this morning.
The opposition BJP and other parties accuse the ruling Congress and Mr Owaisi of using a lengthy medical exam to delay his arrest.
Mr Owaisi's party, the MIM, was an ally of the ruling Congress in Andhra Pradesh till November.
He has been accused by the police of waging war against the state and inciting communal hatred.
Mr Owaisi has sought exemption from questioning for four days on the grounds that the politician is unwell.
Mr Owaisi returned to Hyderabad from London on Monday morning. He was scheduled to appear before the police in a town named Nirmal in the Adilabad district, about 220 kms from Hyderabad. On December 24, he delivered a hate speech here. On YouTube, it metered more than 80,000 views.
Mr Owaisi petitioned the Andhra Pradesh High Court yesterday, asking for the cases against him to be dropped. The petition is likely to be heard on Wednesday.
The government has been criticised for its inaction against the politician. For weeks after his hate speeches were delivered and broadcast on local channels owned partly by other members of his party, there were no cases registered against him.
(With inputs from Agencies)