Police said the ashes were taken from a memorial in central India, where they had been kept since 1948 - the year of Gandhi's assassination by a Hindu extremist.
A portrait of Mahatma Gandhi was also defaced at Bapu Bhawan in Laxmanbagh Sansthan here on Gandhi Jayanti by unidentified persons who wrote "deshdrohi" or traitor over.
Some Hindu hardliners view Gandhi as a traitor for his advocacy of Hindu-Muslim unity.
Police in Rewa, in Madhya Pradesh state, confirmed to BBC Hindi's Shuriah Niazi that they were investigating the theft on the grounds of actions "prejudicial to national integration" and potential breach of the peace.
The theft was 'shameful,' said Mangaldeep Tiwari, caretaker of the Bapu Bhawan memorial, where the ashes were being held.
"I opened the gate of the Bhawan early in the morning because it was Gandhi's birthday," he told Indian website The Wire. "When I returned at around 11pm, I found the mortal remains of Gandhi missing and his poster was defaced."
Police took action after Gurmeet Singh - leader of the local Congress political party - filed a complaint.
"This madness must stop," Mr Singh told The Wire. "I urge Rewa police to check CCTV cameras installed inside Bapu Bhawan."