"We deeply regret that the Indian government felt it was necessary to expel one of our diplomatic personnel," State Department spokeswoman Jen Psaki said in Washington.
Psaki did not identify the US diplomat who has been given 48 hours to leave India.
"This has clearly been a challenging time in the US-India relationship. We expect and hope that this will now come to closure and the Indians will take significant steps with us to improve our relationship and return it to a more constructive place," she said.
Khobragade's Dec 12 handcuffing and strip search for alleged visa fraud triggered outrage in India and led to reprisal withdrawal of diplomatic privileges for the US embassy and consulate in India.
She has returned to India.