"It is absolute rubbish to suggest that this has been done to target South Asian countries," Mr Vaz told the BBC's David Chazan in Dhaka.
But despite the minister's denial that the move was discriminatory, the reports have caused anger in India and Bangladesh.
Mr Vaz, who is on a tour of South Asia, denied that the pilot scheme was specific to the subcontinent and said it would apply to all visitors if successful.
"It is absolute rubbish to suggest that this has been done to target South Asian countries," Mr Vaz told the BBC's David Chazan in Dhaka.
He added that the amount of the bond was still undecided. "No figure has been mentioned as being the amount of the guarantee," Mr Vaz said.
India's warning
India's foreign office reacted icily to the proposal and warned that it could take "reciprocal action".
"The information that we have at present is through press reports as we have not been extended the courtesy of being consulted," Ministry of External Affairs spokesman, Raminder Singh Jassal, said.
However, Britain said the scheme would allow more South Asians to visit Britain.
Home office minister Barbara Roche said a right of appeal would be reinstated for those who are denied visitors' visas because of fears they would try and settle down in Britain illegally.
Criticism
But many critics felt that the plan would hurt poor people as well as ethnic minorities.
"We feel that this project is discriminatory against the black communities of this country," said Ashiki Thanki of the Newham Monitoring Project in London.
"It's clearly an abuse on their freedom to travel, to associate with their families in this country," he added.
The deposit scheme is part of a plan by the British Government to crack down on those who use a visitor's visa to settle down illegally in Britain.
The pilot project is expected to operate through visa offices in India, Pakistan or Bangladesh and could possibly be extended to some African countries later in the year.