Unable to present my accepted paper in conference. Can I now submit the paper to another conference?
On my request, the conference acknowledged that they will not publish
  my paper to their Journals/proceedings. (I've the email transactions
  with the conference secretariat.)


Was the registration for the paper done, i.e. you had paid the registration fee? Was the camera ready version already submitted?

If you had not paid the fee already, then obviously they won't publish your work. In fact, they won't consider for scheduling the program as well. If you had already paid the fee and submitted the CR version, be safe and keep the email transactions with you for possible conflicts in future. However, AFAIK, many conferences don't publish the work unless the registered author presents the paper in the conference. Make sure this is the policy for this conference as well.


  I wish to submit the same paper for an IEEE conference. Is there any
  issue? Please advise.


If you think you are safe in the first question (above), then you could go ahead with submitting to another conference.

You can further view the following related questions in academia SE:


Would my paper be published if I missed the conference due to visa-related problems?
What to do if I can&#39;t get a visa to attend a conference that accepted my paper?
Etiquette when unable to attend a conference


BTW, I had a question, why did you submit the paper to the already-accepted conference at the first place if you were not sure about your attendance? I feel this is not a good sign.