You cannot insist your supplier to charge GST @ 18% on engine which is principal input for Diesel Generating Set. Govt. has made provision for refund on the ground of Inverted Duty Structure. As per the present position of GST law, there is no other option except refund claim as advised by Sh.Alkesh Jani Ji. Classification of both products is O.K.
What I feel that you do not want to face the rigours of filing refund claim on the ground of Inverted Duty Structure every month or quarterly (whatever may be tax period) basis. What you require is not reduction in rate of tax on engine but you require exemption as it was in force In Central Excise era. I draw your attention to Para No.4 of Notification No. 8/2003-CE dated 1.3.2003 as amended up to 26.7.16. That para is reproduced below:
" 4.The exemption contained in this notification shall not apply to specified goods bearing a brand name or trade name, whether registered or not, of another person, except in the following cases :-
where the specified goods, being in the nature of components or parts of any machinery or equipment or appliances, are cleared for use as original equipment in the manufacture of the said machinery or equipment or appliances by following the procedure laid down in the Central Excise (Removal of Goods at Concessional Rate of Duty for Manufacture of Excisable Goods) Rules, 2001 :
Provided that manufacturers, whose aggregate value of clearances of the specified goods for use as original equipment does not exceed rupees one hundred lakhs in the financial year 2002-2003 as calculated in the manner specified in paragraph 1, may submit a declaration regarding such use instead of following the procedure laid down in the said Central Excise(Removal of Goods at Concessional Rate of Duty for Manufacture of Excisable Goods) Rules, 2001;"
The highlighted rule, 2001 were replaced by CENTRAL EXCISE (REMOVAL OF GOODS AT CONCESSIONAL RATE OF DUTY FOR MANUFACTURE OF EXCISABLE AND OTHER GOODS) RULES, 2016 vide [Notification No. 20/2016-C.E. (N.T.), dated 1-3-2016 as amended].
Now in GST there is no such rules. Since tax is being paid on final product by you, you should talk of exemption (on the pattern of above rules) on engine to be used as original equipment in the manufacture of DG Set as it was available in pre-GST era via Notification No.20/16-CE(NT) dated 1.3.16 amending Notification No.34/2001-CE(NT) dated 21.6.2001.
You will have to suggest to GST Council as such provision/facility has been missed while implementing GST. This will also save unnecessary paper work and time involved in getting refund on the basis of Inverted Duty Structure.
If you want relief, you will have to labour hard through Trade and Industry Association.
I hope you have followed what I want to say.