Mr Obama lifted the controversial funding ban in his first week in office
The Vatican has condemned President Obama's move to restore US funding for family planning clinics abroad that give advice on or carry out abortions.
One Vatican official warned against the "arrogance" of those in power who think they can decide between life and death.
Another official said it dealt a blow to groups fighting against "the slaughter of the innocents".
The White House says the move aligns the US with other nations fighting poverty and promoting health care.
On Friday, Mr Obama ended a ban on giving US federal money to international groups that perform abortions or provide information about them.
In an interview published in an Italian newspaper on Saturday, senior Vatican official Monsignor Rino Fisichella urged Mr Obama to listen to all voices in America without "the arrogance of those who, being in power, believe they can decide of life and death."
"If this is one of President Obama's first acts, I have to say, in all due respect, that we're heading quickly toward disappointment," Mr Fisichella, who heads the Vatican's Pontifical Academy for Life, told the Corriere della Sera.
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Another Academy official, Monsignor Elio Sgreccia, said it had dealt a harsh blow to US Catholics and people across the world who are fighting against "the slaughter of the innocents".
The criticism from the Vatican adds to concerns from evangelical Protestant groups that the US decision could presage a wider dismantling of the legal limits of abortion.
Critics of the former funding ban had long argued that it hurt some of the poorest people in the world by denying money to groups that might support abortion, but also work on other aspects of reproductive health care or HIV/Aids.
The ban was first introduced in 1984 by President Ronald Reagan. It was rescinded by President Bill Clinton, before being reinstated by President George W Bush in 2001.