Owino, who spent the night at Pangani Police Station following his arrest on Monday,will be held at Kileleshwa Station pending tomorrow's 10 am ruling.
Appearing at Milimani Law Courts, Mr Owino was charged with two counts, one of subversion and another of uttering abusive words against the President, to which he pleaded not guilty.
The prosecution had called for his detention claiming that he posed a threat to witnesses.
Babu had been accused of inciting violence after his utterances on Sunday the 24th of September during a rally in Dagoretti.
At the rally, the MP is said to have referred to the President as mtoto wa mbwa(puppy), sentiments which were strongly condemned by leaders from different quarters.
Nairobi Woman Representative Esther Passaris condemned the act maintaining it was irresponsible for Owino to refer to the first family in such a derogatory manner.
In a Twitter post addressed to Mama Ngina Kenyatta, she apologised on behalf of the National Super Alliance (NASA), assuring the nation that Owino's sentiments did not represent those of the party.
On Monday, the MP wrote on his Facebook page that he would not apologise because he had not mentioned any names during his address.
I will not apologise to anyone because I called nobody's name during my yesterday's address.
"We have so many Presidents in Kenya, from the President of SONU (Students Organization of Nairobi University) to all presidents of students union in Kenya, President of the Supreme Court, President of Youth Senate and many more," he wrote.
He added that he would stick to objective politics and never abuse people.
Let my brothers and sisters from the Kikuyu nation know that I did not abuse their president. One Kenya one nation."