India has benefitted from a scheme that has seen up to $5.6billion worth of goods enter the U.S. duty-free, but this will end next week on June 5.
Trump has been on a warpath against what he said were high tariffs on U.S. imports to India.
The ministry views this development as part of ongoing issues that "get resolved mutually from time to time" and it would continue to build on its "strong" ties with the US.
But was hopeful, and said, we "will continue to build on our strong ties with the U.S., both economic and people-to-people".
The government on Saturday exuded confidence that India and the USA would continue to work together for further growing ties following Washington's decision to withdraw concessions under the Generalized System of Preferences.
"India had offered resolution on significant United States requests to find a mutually acceptable way forward".
The president removed Turkey from the programme on May 16.
In retaliation for the United States raising tariffs of steel and aluminium imports from India, New Delhi has threatened to increase duties on agricultural products like walnuts, apples and other fruits imported from the US.
"I have determined that India has not assured the United States that India will provide equitable and reasonable access to its markets", he said in a proclamation issued Friday night. "It is unfortunate that this did not find acceptance by the USA", the ministry statement said.
India, which came under the GSP programme in 1975, is its largest beneficiary in the US. "This will remain the guiding factor in the Government's approach", the government said on Saturday, two days after Prime Minister Narendra Modi took the oath for a second term.
The move is the latest push by the Trump administration to reduce USA trade deficits and redress what it considers to be unfair trading relationships with other countries, starting with China.
The Trump administration wants to eliminate special and differential treatment flexibilities for developing countries such as India in the current and future trade negotiations.
To be specific, metal products, machinery and electrical equipment, chemical products would feel the pain the most because these products under the three product classifications make up over 60 per cent of Indian exports - $3.21 billion out of the total $5.6 billion - that availed USA sop.
President Trump had conveyed his intention to terminate India's eligibility for the programme to the USA congress on March 4.
Other sticking points for the USA during discussions included issues related to market access for various agriculture and animal husbandry products and relaxation or easing of procedures related to issues like telecom testing or conformity assessment.
Trump has complained repeatedly that India is a "very very high tariff nation", highlighting in particular New Delhi's taxes against high-end Harley Davidson motorcycles (even after the taxes were cut in half), even though the amount involved is paltry in the overall scheme of things.