Responding to a query by The Straits Times, the ministry said it had not received official notification from India that the review of the pact, officially dubbed the Comprehensive Economic Cooperation Agreement (CECA), had been put on hold.
The report assumes significance as both the sides are facing difficulties in concluding this review.
"India has not put the India-Singapore CECA on hold. It continues (to be) in force," a spokesman of India's Commerce Ministry said in response to a query from The Straits Times.
India's Commerce Secretary Rita Teaotia had recently said there have been difficulties in concluding this review because of certain "small" issues.
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Meanwhile, the National Association of Software and Services Companies (Nasscom) has complained that the movement of Indian software professionals to Singapore had been reduced to a "trickle" since January last year.
The body added that the restrictions are hurting software firms, some of which were even looking to relocate out of Singapore.
The visa issue has been brewing for over a year now, and Nasscom has been engaged in a dialogue with authorities in India as well as Singapore to resolve the matter.
"This is really not keeping with the overall objectives of the Comprehensive Economic Cooperation Agreement (CECA), which is to encourage economic activities in both directions," Nasscom President R Chandrashekhar had said.