The show cause notice to the Jammu and Kashmir Liberation Front chief and a Srinagar-based couple was issued recently by the central probe agency under provisions of the Foreign Exchange Management Act, they said.
The case relates to a 2001 FIR from the Jammu and Kashmir police, which seized USD 1,00,000 (about Rs 48.23 lakh according to conversion rates at the time) from Srinagar -based Mushtaq Ahmad Dar and his wife Shamima alias Shazia aias Bitti.
Dar reportedly told the police that the money was given to him by a person in Nepal to be handed to the JKLF chief.
Malik was arrested in the case but was later let off on bail.
The FEMA notice has been issued after investigators completed their over decade-long probe, officials said.
The agency has asked Malik and the two others to reply to the notice in the next 30 days after which civil adjudication proceedings will begin against them.
Malik was also summoned by the ED in the case but never went.