"This is deplorable," he told reporters outside Parliament when asked to comment on her ill treatment in New York.
The Prime Minister's remarks on the issue came soon after the government asserted in Parliament that India will take strong steps to ensure the return of the 39-year-old diplomat, who was arrested, and restoration of her dignity.
Khobragade was taken into custody on a street in New York.
In Parliament, External Affairs Minister Salman Khurshid condemned the US action and said he will not return to the House if he fails in his responsibility to bring back Khobragade.
He said there was a "conspiracy" in which the 1999-batch IFS officer was "virtually trapped" and maintained that the diplomat is "innocent" and the US action was unwarranted.
"It is not illegality that she is accused of, but the illegality she refused to oblige," he said. Khobragade was taken into custody on a street in New York as she was dropping her daughter to school.
She was released on a USD 250,000 bond after pleading not guilty in court.