The treatment of an Indian diplomat arrested in New York in December triggered a serious spat between the two countries and was widely blamed for the resignation of the U.S. ambassador to India.
The Obama administration has been seeking to revive ties since Modi's election in May, seeing India as a key strategic counter-balance in Asia to an increasingly assertive China.
Modi "conveyed his desire to further deepen and expand the strategic partnership," a statement from the Indian government said.
It said that he hoped for a "forward looking, result-oriented visit" to the United States in September when he is due to attend the United Nations General Assembly in New York.
McCain, who told the Senate last week that Washington should seek to help India's economic and military development, spoke of high expectations about a new momentum in India's economic growth under the new government. There was no mention in the statement of defence deals.
Both governments have signalled they are keen to ramp up bilateral trade, which stands at about $100 billion annually and is considered to be below potential due to disputes over protectionism and intellectual property rights.
McCain's visit comes at an awkward time - just days after reports that the U.S. National Security Agency was authorised to spy on Modi's Bharatiya Janata Party in 2010, when the party was in the opposition.
On Wednesday, foreign ministry summoned a senior U.S. envoy in Delhi and said it had sought an assurance that the surveillance would not happen in the future.
The government statement of their remarks released after the McCain-Modi meeting did not mention the snooping row.
Modi was denied a visa in 2005 for travel to the United States following religious riots in 2002 while he was a state chief minister. Even so, he has responded positively to the U.S. advances and shown no resentment publicly.
In addition to discussing the situation in Iraq and Afghanistan, Modi emphasised that the fight against terror should be a global priority, the statement said.