The ban has been in place since 1994, but officials recently began enforcing it in areas where they say the high birth rate is fuelling ethnic tension.
The tensions led to violent clashes between Buddhist and Muslim communities in the western state last year.
Ms Suu Kyi has been criticised for not speaking up for Rohingya rights.
Tens of thousands of Rohingya Muslims were displaced by the violence and live in temporary camps.
The 1994 ban, that prevents Rohingya Muslims having more than two children, was allowed to lapse in recent years.
But a commission set up to investigate the violence in Rakhine suggested the use of family planning education to address what it described as the rapid growth of the Muslim population.
On Saturday, authorities in Rakhine introduced the two-child policy in two townships, Maung Daw and Bu Thi Daung. It is not clear how it will be enforced.
The vast majority of Rohingya Muslims - about 800,000 people - live in the two townships. Most of those living in camps are elsewhere in Rakhine.
"Under this directive, Bengali [Rohingya] men are allowed to have only one wife and each married couple can have two children. Where there are more than two children, they are considered illegal," Reuters news agency quoted a senior immigration official as saying.
Ms Suu Kyi told reporters she could not confirm whether the policy was being implemented, but if it was, it was illegal.
"It is not good to have such discrimination. And it is not in line with human rights either," she said.
Phil Robertson of the US-based Human Rights Watch (HRW) described the move as outrageous and chilling.
HRW have accused the Burmese authorities of being party to ethnic cleansing during the violence in June and October last year, which left about 200 people dead and up to 140,000 displaced.
The Rohingyas are a stateless group of some 800,000 people who are not recognised as Burmese citizens.
The United Nations describes them as a religious and linguistic minority from western Burma, and one of the most persecuted minorities in the world.
However, many Burmese officials refer to them as Bengalis - a reflection of the widespread belief that this community belong in neighbouring Bangladesh.
Burmese opposition leader Aung San Suu Kyi has condemned a decision by local officials in Rakhine state to enforce a "two-child policy" on Rohingya Muslims.