The United States, Britain and Canada condemned the new law in Africa's most populous nation, with Secretary of State John Kerry saying Monday that it "dangerously restricts freedom" of expression and association of all Nigerians.
Jonathan's spokesman said the president signed the Same Sex Marriage Prohibition Act on Jan. 7, providing penalties of up to 14 years in jail for a gay marriage and up to 10 years' imprisonment for membership or encouragement of gay club, societies and organizations.
The U.N. agency to fight AIDS and the Global Fund to Fight AIDS, Tuberculosis and Malaria expressed "deep concern that access to HIV services for lesbian, gay, bisexual and transgender people will be severely affected by a new law in Nigeria — further criminalizing LGBT people, organizations and activities, as well as people who support them."
The law also criminalizes people and groups who support "the registration, operation and sustenance of gay clubs, societies and organizations, processions or meetings in Nigeria." Those convicted could be jailed for 10 years.
UNAIDS said the law could harm Jonathan's own presidential initiative to fight AIDS, started a year ago.
It said Nigeria has the second largest HIV epidemic globally with an estimated 3.4 million people living with HIV. The disease affects many more gay men than heterosexuals, with 2010 statistics estimating national HIV prevalence at 4 percent compared to 17 percent among gay men, according to UNAIDS.
Jonathan has not publicly expressed his views on homosexuality.
His spokesman, Reuben Abati, told The Associated Press on Monday night, "This is a law that is in line with the people's cultural and religious inclination. So it is a law that is a reflection of the beliefs and orientation of Nigerian people. ... Nigerians are pleased with it."
Associated Press writer Shehu Saulawa contributed to this report from Bauchi, Nigeria.