Ministry of Home Affairs advice (Chennai)

Sorry I know it's not Chennai specific but I don't know what else to do, so please help. My course is supposed to start on June 12th.
I have been struggling for 2 months to obtain a "letter of clearance" from the Ministry of Home affairs so that I can give this to the Indian High Commission in London. The High Commission need this before they can give me a student visa (that's what they told me, anyway).
I believe this is because they are suspicious - it's a small Bible college - but they haven't told me this so I'm just guessing.
So far I have been redirected round the MHA Foreigners Division but in vain. Does anyone know the official procedure for obtaining these "letters of clearance", or the best person in the MHA to contact?
Thanks for your help.