Singh met Naidu, who is also the Chairman of the Rajya Sabha, on the eve of the winter session of Parliament.
Naidu tweeted about the meeting.
Singh is a Congress Rajya Sabha member from Assam.
Earlier this week, Prime Minister Narendra Modi accused Singh of colluding with Pakistan to ensure the BJP's defeat in the Gujarat assembly polls.
Singh hit back at Modi for allegedly spreading "falsehood and canards" to "score political points in a lost cause".
The opposition parties are likely to raise the issue in Parliament.
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