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Pannun, the founder of the banned group Sikhs for Justice (SFJ), holds dual citizenship in Canada and the US.
The official, identified as 39-year-old Vikas Yadav, was reportedly employed by the Cabinet Secretariat, which oversees RAW.
The arrested is Baljeet Singh alias Rana Bhai alias Balli. He is a native of Barwani district in Madhya Pradesh.
SFJ was declared a banned organisation five years ago under the Unlawful Activities (Prevention) Act.
The Federal Bureau of Prisons inmate records on Sunday showed him held at the Metropolitan Detention Centre in Brooklyn.
Judge Mark Jette spoke to the men through an interpreter as he placed them under a no-contact order.
Toronto: Canada is a "rule-of-law country" with a strong and independent justice system and a fundamental commitment to protect its citizens, Prime Minister Justin Trudeau has said, a day after three Indian nationals were charged with the murder of Khalistan separatist Hardeep Singh
The ties between India and Canada came under severe strain following Canadian Prime Minister Justin Trudeau's allegations in September last year.
MEA described the raising of the slogans illustrated the political space given in Canada to "separatism, extremism and violence".
Nikhil Gupta, 52, was charged by federal prosecutors in an indictment unsealed in November last year.