CBI sources said the allegations are that Balakrishna had fudged certain documents and has multiple passports, which is a punishable offence under the Indian Passport Act.
However, the charges were denied by Ramdev-controlled Patanjali Yogapeeth Trust.
"Balakrishna's passport is valid. He had got his passport about 12-13 years back. Why is the government now raising questions about it?" S K Tijarawala, spokesperson of Patanjali Yogapeeth Trust, said.
Besides questions being raised about his nationality, Balakrishna is under scanner of central investigating and law enforcement agencies for allegedly acquiring wealth worth crores of rupees.
"A complaint has been received and we are examining it. It is alleged that Balakrishna has got two passports acquired through illegal means," a CBI official said.
Both Ramdev and Balakrishna were forcibly removed by the Delhi Police on June 4 from Ramlila Ground here where the two were leading a gathering demanding tougher anti-corruption laws and bringing back of black money stashed away abroad.
While Ramdev was moved to Patanjali Yogapeeth, about 20 kms from Haridwar, his associate Balakrishna had gone missing and had surfaced on June 7.
"I am born in Haridwar and I am an Indian. I have completed my education here. My parents are from Nepal," Balakrishna had said on questions about is nationality.