This response is based on the information provided.  We suggest you discuss with your contracting team, program manager and/or legal department as appropriate. 

If you cannot find three responsible sources that you believe can meet your requirement; you, along with the requirements owner, need to review the requirement to ensure it is not unduly restrictive such that it limits competition.  You should also continue market research and broaden your footprint, contact potential firms, etc.  If the requirement is not unduly restrictive and you have done thorough market research, document your contract file in detail with your findings.  With two firms you still have competition; we suggest you present that to the selection authority along with the legal opinion and any relevant Navy policy.