He dared the Maharashtra government to act against him for any violation of law and said the conference was organised after due permission by the state.
Naik is currently being investigated by the NIA for allegedly promoting enmity and hatred between different religious groups in India through his speeches and lectures on various platforms.
"Did Congress save Zakir Naik? Yes I did meet and address a Communal Harmony International Conference organised and addressed by Zakir Naik also in Mumbai," Singh tweeted.
He said the Maharashtra government would have the video recording of speeches by Naik and him in that conference and can act against him.
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"If I have violated any Law, Government of Maharashtra or GOI is free to register a case against me and I am prepared to face any trial," Singh also said.
He, however, questioned those raising fingers at him for meeting Naik.
"But I would like to ask all those who are extremely sensitive of what Zakir Naik speaks. Have they heard inflammatory speeches by Yogi /Hindu Vahini /VHP/Bajrang Dal leaders against Muslims and Christians ?
When asked whether Singh and Ghulam Nabi Azad met Naik, Congress spokesperson Ajoy Kumar said the controversial preacher "also met General Sinha and so many other leaders of BJP but we never hear about it".
"Rather than asking the government, the Opposition is asked this question. To cover its failure, the government continuously get information leaked of 2008 and 2004 to hide its inefficiency and mis-governance.
"My question to you is when will you question the government for their failure. The Government has got no explanation for all their inefficiencies," he said.
"BJP Madhya Pradesh, IT Cell was spying for the ISI. Those are much more interesting stories which could highlight the BJP's involvement," he said.
Naik, 51, left India last year, allegedly to evade arrest after some perpetrators of the Dhaka terror attack claimed that they were inspired by him.
Following the Dhaka attack, the NIA had registered a case against him and some officials of his organisation, Islamic Research Foundation for promoting enmity between different groups on grounds of religion.