Mohammed Jaffer / Mohammed Jaffer / Reuters Devyani Khobragade, who was Indian's deputy consul in New York when she was arrested, has left the U.S.

The Indian deputy consul whose arrest and strip-search in New York touched off a diplomatic spat between the U.S. and India was flying home Friday after being ordered to leave the country.

A federal grand jury charged Devyani Khobragade with visa fraud and making a false statement for allegedly providing bogus information to get papers for a housekeeper she wanted to bring from India to the U.S. and pay less than minimum wage.

She flew from the U.S. late Thursday after refusing to waive her diplomatic immunity and was expected to arrive in New Delhi later Friday, her father told reporters in the Indian capital.

"Her head is held high," said her lawyer, Daniel Arshack. "She knows she has done no wrong and looks forward to assuring the truth is known."

Khobragade was granted diplomatic immunity because the Indian government had moved her from a post at the Indian Consulate in New York to the Indian Mission to the United Nations, a U.S. government official told NBC News.

The U.S. asked for a waiver of that immunity so Khobragade could face the charges against her. India denied the waiver, so the U.S. issued a note requesting Khobragade leave the country immediately.

Her husband and two children were left behind in the U.S. but were expected to follow her to India soon, her father said, according to Reuters.

Khobragade's Dec. 12 arrest — and accompanying strip-search — was denounced by the Indian government as "barbaric." India stripped amenities from the U.S. Embassy there in retaliation.

Secretary of State John Kerry said he had "regrets" that "certain courtesies" were not extended to Khobragade, and India quickly assigned her to a role where she might have fuller diplomatic immunity.

It was not immediately clear wither Thursday’s rapid developments would ease the ill-feeling between New Delhi and Washington.

"We'll focus on one day at a time, today is the day we focus on getting Devyani back," said India's foreign ministry spokesman Syed Akbaruddin, according to Reuters.

In a letter to the court Thursday, U.S. Attorney Preet Bharara said charges against Khobragade would stand until she answered them in court.

The 20-page indictment accuses his client of creating a fake employment contract to obtain a visa for the domestic worker, Sangeet Richard, that claimed she would pay her $9.75 an hour for 40 hours of work a week.

In reality, the grand jury found, Khobragade had negotiated a secret deal with the maid to pay her just $3.33 an hour and ended up paying her less than $2 an hour by making her work 90-plus hours a week with no days off, including sick time.

"On two occasions when the victim became ill, the victim was not given a sick day," the indictment said. "On one occasion, the victim had to ask to see a doctor several times before Khobragade relented. Khobragade told the victim not to get sick because it was expensive."

Andrew Burton / Getty Images file Manhattan U.S. Attorney Preet Bharara

"The victim was routinely called upon at all hours to perform her duties, which included caring for Khobragade's two children, cooking, and cleaning Khobragade's home."

The indictment also alleges that Khobragade, 39, confiscated Richard's passport and refused to return it and refused her requests to quit and return home to India.

In June, Richard left the home and turned to a nonprofit group that supports human trafficking victims, and Khobragade and others launched an intimidation campaign that culminated with the diplomat bringing charges of theft against the maid in India, the court papers say.

Arshack accused investigators of making serious errors in the case, citing Bharara's notice to the court that Khobragade had already left the U.S.

"Dr. Khobragade did not make any false statements and she paid her domestic worker what she was entitled to be paid," Arshack said.

NBC News' Alastair Jamieson and Reuters, contributed to this report.

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