US President Donald Trump has called new Indian tariffs on US products "unacceptable" and demanded that they be withdrawn.
India imposed retaliatory tariffs on 28 US products earlier in June, after the US announced it was withdrawing India's preferential trade treatment.
Mr Trump's criticism came a day after the two sides had downplayed tensions.
He is due to meet Mr Modi on the sidelines of the G20 summit, which begins on June 28 in Osaka, Japan.
Shortly before leaving for Japan, the US President told reporters on the White House lawn that he would be meeting leaders from different countries, "many of whom have been taking advantage of the United States - but not anymore".
Mr Trump's tweet appeared to contradict a joint statement made by India's External Affairs Minister S Jaishankar and visiting US Secretary of State Mike Pompeo on Wednesday.
It said that "even great friends had differences," in what was seen as an attempt to downplay tensions.
US-India bilateral trade was worth $142 billion (£111 billion) in 2018, a sevenfold increase since 2001, according to US figures.
But $5.6 billion worth of Indian exports - previously duty-free in the US - will be hit since the country lost preferential treatment under America's Generalized System of Preferences (GSP) - a scheme that allows some goods to enter the US duty-free.
Trade tensions have been simmering between the two countries. In 2018, India retaliated against US tariff hikes on aluminium and steel by raising its own import duties on a range of goods.
Mr Trump has also threatened to impose sanctions if India purchases oil from Iran and goes ahead with plans to buy Russian S-400 anti-aircraft missiles.