"These allegations have to be throughly enquired into. It is a real shame for all of us that director of a premiere investigative agency has now been charged," Naidu told reporters on sidelines of an event.
The CBI had named Singh along with Qureshi and others in an FIR registered last week for allegedly favouring the meat exporter after receiving a complaint from the Enforcement Directorate.
The agency carried out searches at the residence of Singh yesterday.
"It should be taken to its logical conclusion and whatever links are there should be throughly investigated," he added.
Qureshi has been accused of accepting money from several people for securing favours from public servants.
Meanwhile, asked about BJP's strategy for Brihanmumbai Municipal Corporation (BMC) polls, he said, "Let the results come then we will decide what to do and how to go about it. Why should we make hasty statements now?"
He said BJP is confident of winning the BMC polls.
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