The teenager became the second wife of the 44-year-old in July after an Islamic court gave permission for the pair to wed in the conservative, rural state of Kelantan, local media reported.
It was the latest such case in Malaysia -- there was widespread anger in June after the marriage of an 11-year-old Thai girl to a 41-year-old Malaysian rubber trader, who was also from Kelantan.
While the legal minimum age for marriage in Malaysia is 16, members of the country's Muslim majority can wed at a younger age if religious authorities give approval.
The United Nations on Wednesday put fresh pressure on the Muslim-majority country to halt such unions.
"It's unacceptable that yet another child has got married to an elder man," said Marianne Clark-Hattingh, Malaysia representative of U.N. children's agency UNICEF, adding it was urgent to "bring legislative change to ban the practice".
Deputy Prime Minister Wan Azizah Wan Ismail, whose portfolio includes women's issues, said that welfare officers had been sent to meet the girl, reportedly one of 13 siblings, and her parents in the district of Tumpat.
However she suggested there was little the government could do to stop the union, as Islamic courts have jurisdiction over the issue of marriage between Muslims.
Under Malaysia's dual-track legal system, Islamic courts can handle religious and family matters for Muslims, who make up about 60 percent of the country's 32 million inhabitants.
The girl's father was quoted in The Star newspaper as saying that he had agreed for his daughter to be wed as he did not want her to continue living in poverty, and insisted she was "happily married."
The young bride said she agreed to the marriage, although she had known the man for only a few months.
"I am happy, and I will try to keep my husband happy. That is all that matters to me," she told the paper.
In the June case, the 11-year-old married the Malaysian man in Thailand's Muslim-majority south under religious laws, becoming his third wife. Following an outcry, the girl returned to Thailand last month.