Trump signed a decree barring US funding for foreign non-governmental groups that provide abortion assistance or engage in advocacy.
The Microsoft founder and billionaire philanthropist runs the Bill and Melinda Gates Foundation with his wife, focusing on health and education worldwide.
"We're concerned that this shift could impact millions of women and girls around the world," Melinda Gates told the British daily.
"Enabling women to time and space their pregnancies and providing access to treatment and prevention of infectious diseases is life-saving work," she said.
"It saves moms' lives and it saves babies' lives, and that has long had wide support in the United States".
Bill Gates said the funding cut would "create a void that even a foundation like ours can't fill".
"The US is the No1 donor in the work that we do. Government aid can't be replaced by philanthropy."
Trump last month signed a decree barring US funding for foreign non-governmental groups that provide abortion assistance or engage in advocacy, relaunching a battle that has long divided Americans.
The restrictions were first put in place in 1984 by Republican president Ronald Reagan.
Later eliminated by Democratic president Bill Clinton, they were reinstalled by his Republican successor George W. Bush, and annulled again after Barack Obama took office.
Trump's version goes further because it applies to any organisation that receives funding from US Aid, not just those involved in family planning.