Shanks, speaking to BBC Radio Scotland Breakfast, said he had arranged for Swinney to have a security briefing following his comments in April.
He said it was therefore “surprising” that “having had that security briefing” the first minister was continuing to pursue the matter.
The Scottish Labour MP told the programme: “I think it is for him [Swinney] to answer why he is balancing what seems to be a political intervention against the country’s national security.
“I think it is irresponsible for the first minister to do that.”
He added: “There is no inherent reason why the UK government would not want to see jobs created in the north of Scotland either, so I hope people would take it on face value when I say there are national security implications.
“That is a legitimate reason for us to say no to a particular investment.”
Ardersier is a former oil and gas fabrication yard which at its peak employed about 4,500 people, before closing in 2001 as demand dropped.
The 450-acre (182ha) site is currently being redeveloped and forms part of the Inverness and Cromarty Firth Green Freeport.
