The need for a clarification arose after three jawans of the Jammu and Kashmir Light Infantry were arrested on Tuesday by Military Intelligence.
The controversy erupted last week when the Times Now television channel telecast a report based on a letter written by National Security Advisr M K Narayanan in November 2005 that the Indian Air Force had been infiltrated by Lashkar terrorists.
The IAF is learnt to have ordered a probe into the issue.
Home Minister Shivraj Patil told Parliament on Wednesday that the three men arrested on Tuesday were not members of the Indian Army.