The Navratna company had posted a net profit of Rs 55.91 crore in the year-ago period.
However, total income during April-June rose to Rs 900.87 crore, from Rs 861.73 crore in the same quarter a year ago.
Its total expenses were at Rs 892.59 crore as against Rs 789.07 crore in the June 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.