The facility has now been "scrapped permanently," said Muhyideein Yassin.
Apart from Indians, the VOA facility was extended to tourists from China, Bhutan, Nepal, Bangladesh, Myanmar, Taiwan and Comoros.
Thousands of tourists had abused their VOA, which was introduced in 2006 in conjunction with Visit Malaysia 2007, by overstaying.
The government suspended the facility in Feb 2010 for visitors from India following reports that the highest number of VOA abuse involved citizens from India.
Earlier, Prime Minister Najib Tun Razak had also expressed concern over the "disappearance" of almost 40,000 Indians who had entered the country through the VOA.