Goods in Transit is very normal for any business entity.

If Good started from your vendor on 28th June 2017 from Maharashtra, and reach your factory on 3rd July 2017. This is called Goods in Transit as on 30-6-2017

So, The Government has given a simple method to deal with this.

In Short : Take the GST in July for this.

Detailed Explanation : Legal Extracts

Section 140 (5) of CGST Act.

A registered person shall be entitled to take, in his electronic credit ledger, credit of eligible duties and taxes in respect of inputs or  input services  received on or after the appointed day but the duty or tax in respect of which has been paid by the supplier under the existing law, subject to the condition that the invoice or any other duty or tax paying document of the same was recorded in the books of account of such person within a period of thirty days from the appointed day:ABC 

Question : Is this for all valid goods in Transit   :

Answer : Yes

Question : Is this also valid for services bills ?  

Answer is Yes. example . Your ISO9001 consultant, made a bill in April 2017, you book it in July 2017. It is ok and valid. Same for your Chartered Accountant, your Telephone bill company and every other service valid for ITC.

Question : What are the conditions ?

Bill is dated prior to the 30-6-17, and you book it after 30-6-2017

Question : It is receipt of goods or booking of bill ?

Answer : The Condition is Booking of the Bill in your books of accounts

Question : Should I take this Modvat in the 30th June return ?

Answer : No, you cannot. Since you have not received the Material at your gate

Question : Where will I get the Modvat / ITC ?

Answer : You will get this in the month of July 2017. This is a part of the Transition Provisions. This is a part of the CGST Act itself. Google search for the Section 140(5) CGST Act. It is plainly written there. See the extract of this, pasted above

Question : What will be its treatment in Finsys ?

Finsys will pass this as a Purchase Voucher. Finsys will automatically calculate the GST on this as per current law. However since the paper invoice from the vendor will carry the Excise @12.5% ( in this example) so, you will manually edit this voucher  as under.

Purchase Raw Material             Debit  100000

GST ( Transition Excise )         Debit     12500

GST ( Transition VAT/CST )             Debit       xxxx

To Creditor Vendor Account                                xxxxxx

Regarding the Excise law is fully clear that ITC will be received. However for the CST, it is expected to be received. But the department is yet to clarify on the same as on 3-7-2017 at 5.22pm.

Source : CBEC Website : Trasistion Provisions / Rules

http://www.cbec.gov.in/resources//htdocs-cbec/gst/transition-rules-04062017.pdf;jsessionid=3D0DA26D48092D2EAD73B293CA6FE7B4

Rule 1. Tax or duty credit carried forward under any existing law or on goods held in stock on the appointed day

Para 2 (c) in the case of a claim under sub-section (5) of section 140, furnish the following details— (i) the name of the supplier, serial number and date of issue of the invoice by the supplier or any document on the basis of which credit of input tax was admissible under the existing law, (ii) the description and value of the goods or services, (iii) the quantity in case of goods and the unit or unit quantity code thereof, (iv) the amount of eligible taxes and duties or, as the case may be, the value added tax [or entry tax] charged by the supplier in respect of the goods or services, and (v) the date on which the receipt of goods or services is entered in the books of account of the recipient.

Para (3) The amount of credit specified in the application in FORM GST TRAN-1 shall be credited to the electronic credit ledger of the applicant maintained in FORM GST PMT-2 on the Common Portal.

Final Answer

Hence, you have to declare the same on the portal in this form GST Tran-1. And Relax.  and in Finsys, your Gate Entry as usual, MRR as usual, QC as usual, GST entry ( to be done ... but with some change ... not taken). Make the Purchase Voucher., edit it to match the entry shown above.