This comes after the Karnataka government initiated a move for a separate flag for the state with Chief Minister Siddaramaiah defending the step after it came under attack from rival parties.
"We are one nation, one flag. Legally there is no provision either for providing or prohibiting a separate flag for any state," a home ministry spokesperson said.
Home ministry officials said Karnataka already has a flag which represents only the "people and not the government".
But the use of that flag was also challenged in courts by some people and a decision on the matter is yet to be taken, the official, who wished not to be quoted, said.
A nine-member committee has been formed by Karnataka's Congress government and tasked with submitting a report on designing the separate flag for the state and providing a legal standing for it.
If the flag comes into being, Karnataka will be the second state to have its official flag after Jammu and Kashmir, which enjoys a special status under Article 370 of theConstitution.