"We certainly urge all our allies, our partners to move away from Russian equipment ... and really avoid any kind of acquisitions that would trigger sanctions on our behalf," Austin told reporters in New Delhi.
No S400 systems have been delivered to India and so the possibility of sanctions was not discussed, he said.
India made an initial payment of $800 million in 2019 towards the Russian purchase and the first set of missile batteries are expected later this year.
Ahead of Austin's trip, Senator Bob Menendez, chairman of the US Senate Foreign Relations Committee, asked him to raise democracy and human rights concerns in his talks with the Indian government, as well reaffirm the Biden administration's opposition to India's planned purchase of the Russian systems.
Austin is making the first visit by a top member of US President Joe Biden's administration to India as part of efforts to forge an alliance of countries seeking to push back against China's assertiveness in the region.
The leaders of the United States, India, Australia and Japan - countries together known as the Quad - held a first summit last week pledging to work together for a free and open Indo-Pacific and to cooperate on maritime and cyber security in the face of challenges from China.
Austin met Indian Prime Minister Narendra Modi on his arrival in New Delhi on Friday. He leaves on Sunday.
India drew closer to the United States last year following a deadly border clash with China. Washington has helped New Delhi, leasing surveillance drones and supplying cold-weather gear for Indian troops.
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