The Navratna company had posted a net loss of Rs 17.77 crore in the year-ago period.
However, total income during July-September rose to Rs 824.86 crore, from Rs 806 crore in the same quarter a year ago.
Its total expenses were also higher at Rs 883.04 crore as against Rs 806.02 crore in the September quarter last fiscal.
As the country's premier shipping line, the SCI owns and operates around one-third of the Indian tonnage, and has operating interests in practically all areas of the shipping business servicing, both national and international trades.