The Karachi protest attracted 19 activist and women's groups
He said that rape was a "money-making concern" and many argued it was a way to get money and a visa to emigrate.
Pakistan's most-high profile rape victim, Mukhtar Mai, told the BBC no woman could subject herself to "such a horrendous experience" to make money.
Women's groups and activists protested in Karachi on Friday, shouting: "Down with chauvinism".
'Money for justice'
The president made his comments in an interview with the Washington Post on 13 September, incensing campaigners and others at home.
"You must understand the environment in Pakistan. This has become a money-making concern," he said.
"A lot of people say if you want to go abroad and get a visa for Canada or citizenship and be a millionaire, get yourself raped."
PRESIDENT MUSHARRAF A lot people say if you want to go abroad... get yourself raped
In Karachi on Friday, 19 rights and advocacy groups vented their anger at the remarks, holding banners such as: "Who wants to be a millionaire - just get raped!"
Sumar Mallah, a fisherman whose five-year-old daughter was raped and killed on 5 September, was at the rally.
Mr Mallah said: "The police and the rapists have been insisting that I accept money and forget about my daughter. I will never settle for money. I want justice."
Activist Fauzia Burney said: "General Musharraf's remarks are so shocking because they are so removed from reality."
Mukhtar Mai, who shot to world attention after being gang raped in 2002, allegedly on the orders of a village council or panchayat, earlier told the BBC: "I offer all the riches I've made out of the panchayat-enforced gang-rape to the president in return for justice."
The Women's Action Forum described the president's comments as "outrageous".
Last week President Musharraf told a conference on violence against women in Islamabad that Pakistan should not be singled out for its treatment of women.
He also lashed out at rights groups for their role in highlighting cases such as Ms Mai's outside the country. Leading rights groups called the conference a "farce".
The president's critics say he pays only lip service to cracking down on the abuse of women, hundreds of whom are raped and murdered every year in so-called honour cases in Pakistan.
Despite government protestations that it is doing much to help women, many of those who try to register cases of rape and violence find it as hard as ever to do so, campaigners say.
Sparking controversy and eliciting widespread condemnation in an interview with the Washington Post, Pakistan's President, Pervez Musharraf, has made some poorly-judged comments about rape and rape victims.

Musharaff was quoted as having said, "Rape has become a money-making concern" and he suggested that getting raped was a method of getting a visa to western countries.

Activists and opposition MPs alike condemned Musharaff's comments.  The high-profile rape victim, Mukhtar Mai, dismissed the idea that any woman could allow herself to be subjected to such treatment for money.  Her case attracted widespread international media attention with it being alleged that her rape was ordered by the local panchayat (town council).