"Perhaps through marriage they can lead a healthier, better life," he said, according to news agency.
"And the person who was raped will not necessarily have a bleak future. She will have a husband at least, and this could serve as a remedy to growing social problems."
Sharmila Sekaran, who heads the advocacy group Voice of the Children, told the Guardian that she was "outraged"over Shabudin's statement, which was "basically to justify and legalise a wrong - a statutory rape."
Sekaran said: "He's a leader of society, as a member of parliament, and it's worrying that he has this line of thinking. It does send a message across the country that it is something that we are supposed to be okay with. That's a very worrying trend: 'Go and rape someone and if you get caught offer to marry them."'
Government minister Dato' Abdul Rahman Dahlan said the notion that rapists should marry their victims, many who are underage, struck him with "utter shock and disappointment".
"Every child has the right to live, to dream, and to have fun," Abdul Rahman, a minister in the Prime Minister's Department, wrote on Facebook.
"While it is the parents' responsibility to provide a decent childhood for their children, the Government and lawmakers have the responsibility to protect the best interest of Malaysian children.
"It is with that conviction (SIC) in mind that I believe laws are enacted to protect our children - especially underage girls. The laws is unequivocal on this matter, according to Malaysian Penal Code Section 375 (g) it is considered statutory rape for a man to have sex with a girl under 16 years of age - with or without her consent. Therefore, it is abhorrent (SIC) in this 21st century to suggest that a rapist - who should in the first place be prosecuted - has the means to escape legal responsibility simply by marrying his victim."
Penang's Chief Minister, Lim Guan Eng, called for Shabudin to step down, saying his suggestion that rapists should be permitted to marry their victims shows a "depraved and sick" mind.
"Penangites don't want a monster to become their MP, we don't want people with no compassion for rape victims to be an MP," he said at a news conference. "We are ashamed to have an MP like this from Penang. Even though he's not in the state government, he is a black mark for Penang."
Following an international uproar, the Malaysian MP said in a statement on Facebook that his comments had been misconstrued.
Reuters reported that Shabudin said he only opposed the ban on child marriages because it went against provisions in sharia law - adding that marriage is not a "back door exit to legalise rape".