The match is scheduled as a home fixture for Nigeria, who are finalising their preparations ahead of the World Cup in Brazil which starts on June 12.
"We are liaising with the relevant authorities and will prepare for the match as normal," a Scottish FA spokesman said on Tuesday.
A spokesman for the NCA refused to comment, saying: "The NCA will from time to time provide operational detail necessary for public reassurance purposes.
"It does not routinely confirm or deny the existence of specific operations or provide ongoing commentary on operational activity."
The fixture is set to go ahead, with Nigeria coach Stephen Keshi telling Sky Sports News: "We're not part of this. We don't know anything about this. We're here to play."
Nigeria striker Peter Odemwingie, based in England with Premier League side Stoke, added: "This is the first time I'm hearing it. I'm with the players every minute, every day, we don't hear of this."