"We lose a lot of money in civil claims when we arrest without proper due diligence", said Mbalula.
Mbalula said the case against Manana was "very disappointing".
Addressing the media in Cape Town on issues of crime against women, Minister of Police Fikile Mbalula said no-one was above the law and Manana would not receive special treatment.
She also reportedly opened a case with the police against the Deputy Minister.
It appears he entered the court through the parking entrance for staff.
Manana appeared briefly at the Randburg Magistrate's Court, where he spent most of the morning and afternoon waiting as the National Prosecuting Authority (NPA) prepared his docket. "Nonetheless, everybody is presumed innocent until proven otherwise".
"I've helped over 5,000 women who have alerted me of abuse".
The DA and the EFF have asked President Jacob Zuma to fire Manana. I could also opt to stand down.
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Mbalula said he would need to get answers on Manana's VIP protection, as they essentially reported to him as police minister. However, he was not arrested before his court appearance.
He said Manana's admission of guilt on tape was part of the evidence gathered, along with witness statements.
"Your state fully supports the victim and acts only on behalf of the victim", said Mbalula.
Legal expert, Ulrich Roux also says the public expects Manana to be treated like everyone else.
"This assault is a shocking indictment on Manana and he must now face the full might of the law", said the party's spokesperson on higher education and training, Hlomela Bucwa. He ultimately made a decision to hold the press conference because the issue had become a public issue, and to avoid accusations of special treatment.
In an "unreserved" apology to Mandisa and her family on Monday, Manana said he would co-operate fully with the legal process.
"There is something wrong in terms of the administering of justice at a police station level".