India slapped higher tariffs on 28 U.S. products following Washington's withdrawal this month of key trade privileges for New Delhi.
"I look forward to speaking with Prime Minister Modi about the fact that India, for years having put very high tariffs against the United States, just recently increased the tariffs even further," Trump said on Twitter.
"This is unacceptable and the tariffs must be withdrawn!" said Trump, who will meet Indian Prime Minister Narendra Modi at this week's G20 summit in Japan.
India's trade ministry did not immediately respond to a Reuters email seeking comment.
Trump's remarks could further worsen a trade row that has led to tit-for-tat tariffs from India and the United States and created an unease over the depth of their security alliance.
U.S. Secretary of State Mike Pompeo, who was in New Delhi on Wednesday, sought to reduce heightened trade tension with India, promising a renewed focus on negotiating better ties, but giving few specifics of how they would overcome disputes over trade and investment.
Trump scrapped trade privileges for India under the Generalized System of Preferences (GSP), under which New Delhi was the biggest beneficiary that allowed duty-free exports of up to $5.6 billion.
India initially issued an order in June last year to raise import taxes as high as 120% on a slew of U.S. items, incensed by Washington's refusal to exempt it from higher steel and aluminium tariffs.
But New Delhi repeatedly delayed raising tariffs as the two nations engaged in trade talks. Trade between them stood at about $142.1 billion in 2018.