Once the CST (Central sales tax) is phased out, optimisation of warehouses and inventories will accrue in savings on logistics.
The elimination of check posts will also help deliver savings as goods move faster, the agency said, pointing out that the consumer durables sector will benefit the most.
"Manufacturers of non-bulk goods spend about 5-8 per cent of sales on logistics. Goods & services tax (GST) will save warehousing costs of 1-1.5 per cent of sales over the next three-four years.
This will amount to a saving of up to 20 per cent on the total cost of logistics for companies, he added.
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Those in favour of GST, which will make the entire country a single market, believe that the move will help push GDP by up to 2 per cent in the medium term. However, the annual incremental GDP will be around 20 basis points only.
Crisil said a complete phase out of CST is necessary for enjoying the benefits on the logistics side.
It added that at present, 25 per cent of the journey time is wasted at the various check posts and city entry points, which results in higher cost of operations as well as forces companies to maintain buffer inventories.
On the benefits side, Crisil said the consumer durables sector, which has the most number of warehouses set up solely to avoid paying CST, stand to potentially save 30 per cent of their logistic costs.
In the Budget, Finance Minister Arun Jaitley had promised that GST would be rolled out from April 1, 2016. The GST Bill after being passed by the Lok Sahba has been sent to the select panel of the Rajya Sabha after the Opposition objected to the changes the government brought into the previous Bill and is likely to be taken up again in the forthcoming Monsoon session.