Thank you very much to my professional colleagues to adding various perspectives on the issue/s under discussion. I find them deeply engaging.
Please allow me to add my two cents (strictly as part of ongoing academic discussion):
A. Section 129 (1) reads as under:
"Notwithstanding anything contained in this Act, where any person transports any goods or stores any goods while they are in transit in contravention of the provisions of this Act or the rules made thereunder, all such goods and conveyance used as a means of transport for carrying the said goods and documents relating to such goods and conveyance shall be liable to detention or seizure and after detention or seizure, shall be released
.................."
B. As said earlier, "Mens Rea" is NOT an essential requirement for imposing penalty u/s 129 in my view.
C. However, for levying penalty u/s 129 (1), there has to be a transportation of goods (or storage in transit) in contravention of act & rules thereunder.
C1. In other words, the activity of transportation of goods (by itself) should be in contravention of act & rules made thereunder for imposing penalty u/s 129(1). Each & every contravention of act / rules can not result into proceedings u/s 129 unless and until such contravention is inter-linked with the activity of transportation.
(For subsequent part of this post, situation/s about 'storage in transit' are ignored to limit scope of this discussion.)
D. Till the time, goods are duly accompanied by a valid E-way Bill & valid tax-invoice (or other valid documents, at the case may be) (In other words, when Rule 138A is complied with), no penalty can be imposed u/s 129.
D1. But of course, above position is subject to Rule 138B & 138C. If Description of goods & quantity of goods (as declared in accompanying documents u/r 138A) matches with actual goods during 'Inspection and verification of goods' by Dept. officers, same should be sufficient.
D2. Subject to compliance with Rule 138A, If any discrepancy is noticed by Dept. during 'Verification of documents and conveyances u/r 138B' OR during 'Inspection and verification of goods u/r 139C' where tax-payer can give 'logical, bonafide & reasonable explanation' (Please note that what I meant here, is explained below more elaborately), no penalty can be imposed u/s 129.
D3. This position remains even if above-said 'logical, bonafide & reasonable explanation' is found to be contrary to law & rules made thereunder.
D4. This is because such situation, in my view, are NOT falling under 'a transportation of goods in contravention of act & rules thereunder', which is pre-requisite to impose penalty u/s 129.
D5. Kindly note that I am NOT using means rea defence while sharing above views. I am just explaining scope of proceedings u/s 129 to the best of my understanding.
D6. But, What is 'logical, bonafide & reasonable explanation' will vary in each & every case depending upon nature of discrepancy observed. One should NOT generalise the same OR over-extent the principal I am trying to explain here.
D6.1 What is important is to note & understand the scope of proceedings u/s 129 first and then, evaluate whether tax-payer has given 'logical, bonafide & reasonable explanation' or not in a particular scenario.
D6.2. Let me give you some example to explain my thought process:
I) During inspection by Dept., everything is found in order except the fact that against "1,00,000 Nos' of declared goods, only "99,500 Nos' of goods were found. For reasons given above, no proceedings can be initiated u/s 129.
II) During inspection by Dept., everything is found in order except the fact that against "1,00,000 Nos' of declared goods, "1,00,500 Nos' of goods were found. For reasons given above, proceedings can be initiated u/s 129 but only for excess quantity of goods (i.e. 500 Nos.) & not for entire quantity of goods (i.e. 1,00,500 Nos) so found. But explanation like human error / bonafide mistake by loading staff etc. will NOT be 'logical, bonafide & reasonable explanation' to avoid proceedings u/s 129 altogether.
III) During inspection by Dept., everything is found in order except the fact that HSN used was wrong even though there is no dispute raised about accuracy of 'description of goods & tax-payable' as disclosed in accompanied E-way Bill & Tax-Invoice. For reasons given above, no proceedings can be initiated u/s 129.
IV) During inspection by Dept., everything is found in order except the fact that Dept. "suspects" (without any evidence) that subject goods are highly undervalued. For reasons given above, no proceedings can be initiated u/s 129.
V) During inspection by Dept., everything is found in order except the fact that there is difference in taxable value & tax-payable between valid E-way Bill & valid E-Invoice accompanying the goods. For reasons given above, no proceedings can be initiated u/s 129.
VI) During inspection by Dept., goods were found materially different than what is declared in valid E-way Bill & valid invoice accompanying them (For example, actual goods were 'cigarettes' where declared goods as per E-way Bill & Invoice were 'Rice'). This is fit case for proceedings u/s 129 (as there cannot be any 'logical, bonafide & reasonable explanation' for given situation).
VII) During inspection by Dept., everything is found in order except the fact that there is genuine dispute across industry about HSN & rate of taxes applicable to goods in transit. Here, tax-payer can give 'logical, bonafide & reasonable explanation' to support HSN & rate of tax used by him. Hence, no penalty can be imposed u/s 129 even if the dispute about 'HSN & rate of taxes applicable to subject goods' is subsequently settled in favour of Revenue by Court.
D7. For the discrepancy so noticed by Dept. (where penalty u/s 129 cannot be imposed, due to reasons explained above), proceedings under other provisions of Act (For example: Section 73, 74, 122, 125 etc., depending upon facts of each case) can be initiated by Revenue being allowed (& actually required) under the Act.
As said at the start, please treat this post as pure academic discussion and nothing beyond.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.